Warning: Permanently added '2620:52:3:1:dead:beef:cafe:c15a' (ED25519) to the list of known hosts.

You can reproduce this build on your computer by running:

  sudo dnf install copr-rpmbuild
  /usr/bin/copr-rpmbuild --verbose --drop-resultdir --task-url https://copr.fedorainfracloud.org/backend/get-build-task/7508323-fedora-39-x86_64 --chroot fedora-39-x86_64


Version: 0.73
PID: 23053
Logging PID: 23054
Task:
{'allow_user_ssh': False,
 'appstream': False,
 'background': True,
 'build_id': 7508323,
 'buildroot_pkgs': [],
 'chroot': 'fedora-39-x86_64',
 'enable_net': False,
 'fedora_review': False,
 'git_hash': '5c68f6a9db36083946686b5cb383a461971aec92',
 'git_repo': 'https://copr-dist-git.fedorainfracloud.org/git/psimovec/openblas-0.3.23/mmseq',
 'isolation': 'default',
 'memory_reqs': 2048,
 'package_name': 'mmseq',
 'package_version': '1.0.11-19',
 'project_dirname': 'openblas-0.3.23',
 'project_name': 'openblas-0.3.23',
 'project_owner': 'psimovec',
 'repo_priority': None,
 'repos': [{'baseurl': 'https://download.copr.fedorainfracloud.org/results/psimovec/openblas-0.3.23/fedora-39-x86_64/',
            'id': 'copr_base',
            'name': 'Copr repository',
            'priority': None},
           {'baseurl': 'http://kojipkgs.fedoraproject.org/repos/rawhide/latest/$basearch/',
            'id': 'http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch',
            'name': 'Additional repo http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch'}],
 'sandbox': 'psimovec/openblas-0.3.23--https://src.fedoraproject.org/user/churchyard',
 'source_json': {},
 'source_type': None,
 'ssh_public_keys': None,
 'submitter': 'https://src.fedoraproject.org/user/churchyard',
 'tags': [],
 'task_id': '7508323-fedora-39-x86_64',
 'timeout': 18000,
 'uses_devel_repo': False,
 'with_opts': [],
 'without_opts': []}

Running: git clone https://copr-dist-git.fedorainfracloud.org/git/psimovec/openblas-0.3.23/mmseq /var/lib/copr-rpmbuild/workspace/workdir-xx_bwfy8/mmseq --depth 500 --no-single-branch --recursive

cmd: ['git', 'clone', 'https://copr-dist-git.fedorainfracloud.org/git/psimovec/openblas-0.3.23/mmseq', '/var/lib/copr-rpmbuild/workspace/workdir-xx_bwfy8/mmseq', '--depth', '500', '--no-single-branch', '--recursive']
cwd: .
rc: 0
stdout: 
stderr: Cloning into '/var/lib/copr-rpmbuild/workspace/workdir-xx_bwfy8/mmseq'...

Running: git checkout 5c68f6a9db36083946686b5cb383a461971aec92 --

cmd: ['git', 'checkout', '5c68f6a9db36083946686b5cb383a461971aec92', '--']
cwd: /var/lib/copr-rpmbuild/workspace/workdir-xx_bwfy8/mmseq
rc: 0
stdout: 
stderr: Note: switching to '5c68f6a9db36083946686b5cb383a461971aec92'.

You are in 'detached HEAD' state. You can look around, make experimental
changes and commit them, and you can discard any commits you make in this
state without impacting any branches by switching back to a branch.

If you want to create a new branch to retain commits you create, you may
do so (now or later) by using -c with the switch command. Example:

  git switch -c <new-branch-name>

Or undo this operation with:

  git switch -

Turn off this advice by setting config variable advice.detachedHead to false

HEAD is now at 5c68f6a automatic import of mmseq

Running: copr-distgit-client sources

/usr/bin/tail:   % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
100 2781k  100 2781k    0     0  19.4M      0 --:--:-- --:--:-- --:--:-- 19.5M
INFO: Reading stdout from command: md5sum 1.0.11.zip

/var/lib/copr-rpmbuild/main.log: file truncated
Running (timeout=18000): unbuffer mock --spec /var/lib/copr-rpmbuild/workspace/workdir-xx_bwfy8/mmseq/mmseq.spec --sources /var/lib/copr-rpmbuild/workspace/workdir-xx_bwfy8/mmseq --resultdir /var/lib/copr-rpmbuild/results --uniqueext 1717081834.800473 -r /var/lib/copr-rpmbuild/results/configs/child.cfg
INFO: mock.py version 5.6 starting (python version = 3.12.1, NVR = mock-5.6-1.fc39), args: /usr/libexec/mock/mock --spec /var/lib/copr-rpmbuild/workspace/workdir-xx_bwfy8/mmseq/mmseq.spec --sources /var/lib/copr-rpmbuild/workspace/workdir-xx_bwfy8/mmseq --resultdir /var/lib/copr-rpmbuild/results --uniqueext 1717081834.800473 -r /var/lib/copr-rpmbuild/results/configs/child.cfg
Start(bootstrap): init plugins
INFO: tmpfs initialized
INFO: selinux enabled
INFO: chroot_scan: initialized
INFO: compress_logs: initialized
Finish(bootstrap): init plugins
Start: init plugins
INFO: tmpfs initialized
INFO: selinux enabled
INFO: chroot_scan: initialized
INFO: compress_logs: initialized
Finish: init plugins
INFO: Signal handler active
Start: run
INFO: Start(/var/lib/copr-rpmbuild/workspace/workdir-xx_bwfy8/mmseq/mmseq.spec)  Config(fedora-39-x86_64)
Start: clean chroot
Finish: clean chroot
Mock Version: 5.6
INFO: Mock Version: 5.6
Start(bootstrap): chroot init
INFO: mounting tmpfs at /var/lib/mock/fedora-39-x86_64-bootstrap-1717081834.800473/root.
INFO: calling preinit hooks
INFO: enabled root cache
INFO: enabled package manager cache
Start(bootstrap): cleaning package manager metadata
Finish(bootstrap): cleaning package manager metadata
INFO: Guessed host environment type: unknown
INFO: Using bootstrap image: registry.fedoraproject.org/fedora:39
INFO: Pulling image: registry.fedoraproject.org/fedora:39
INFO: Copy content of container registry.fedoraproject.org/fedora:39 to /var/lib/mock/fedora-39-x86_64-bootstrap-1717081834.800473/root
INFO: Checking that registry.fedoraproject.org/fedora:39 image matches host's architecture
INFO: mounting registry.fedoraproject.org/fedora:39 with podman image mount
INFO: image registry.fedoraproject.org/fedora:39 as /var/lib/containers/storage/overlay/dd7e1b244ba184adc65f51b3cf8d611421d7bdad62b1db5b388cd3e172f42fcb/merged
INFO: umounting image registry.fedoraproject.org/fedora:39 (/var/lib/containers/storage/overlay/dd7e1b244ba184adc65f51b3cf8d611421d7bdad62b1db5b388cd3e172f42fcb/merged) with podman image umount
INFO: Package manager dnf detected and used (fallback)
INFO: Bootstrap image not marked ready
Start(bootstrap): installing dnf tooling
No matches found for the following disable plugin patterns: local, spacewalk, versionlock
Copr repository                                  39 MB/s |  19 MB     00:00    
Additional repo http_kojipkgs_fedoraproject_org  39 MB/s |  75 MB     00:01    
fedora                                           29 MB/s |  89 MB     00:03    
updates                                          13 MB/s |  38 MB     00:02    
Last metadata expiration check: 0:00:04 ago on Thu May 30 15:11:23 2024.
Package python3-dnf-4.19.2-1.fc39.noarch is already installed.
Dependencies resolved.
=========================================================================================================================
 Package                    Arch    Version          Repository                                                      Size
=========================================================================================================================
Installing:
 dnf5                       x86_64  5.2.2.0-1.fc41   http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch  692 k
     replacing  dnf.noarch 4.19.2-1.fc39
     replacing  yum.noarch 4.19.2-1.fc39
 python3-dnf-plugins-core   noarch  4.7.0-1.fc41     http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch  302 k
Upgrading:
 dnf-data                   noarch  4.20.0-1.fc41    http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   39 k
 libstdc++                  x86_64  14.1.1-4.fc41    http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch  884 k
 python3-dnf                noarch  4.20.0-1.fc41    http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch  580 k
Installing dependencies:
 dbus-libs                  x86_64  1:1.14.10-3.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch  156 k
 fmt                        x86_64  10.2.1-4.fc41    http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch  125 k
 libdnf5                    x86_64  5.2.2.0-1.fc41   http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch  1.0 M
 libdnf5-cli                x86_64  5.2.2.0-1.fc41   http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch  306 k
 python3-dateutil           noarch  1:2.8.2-13.fc40  http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch  345 k
 python3-dbus               x86_64  1.3.2-6.fc40     http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch  145 k
 python3-distro             noarch  1.9.0-3.fc40     http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   45 k
 python3-six                noarch  1.16.0-14.fc40   http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   41 k
 python3-systemd            x86_64  235-9.fc40       http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch  100 k
 sdbus-cpp                  x86_64  1.5.0-2.fc41     http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch  113 k

Transaction Summary
=========================================================================================================================
Install  12 Packages
Upgrade   3 Packages

Total download size: 4.8 M
Downloading Packages:
(1/15): fmt-10.2.1-4.fc41.x86_64.rpm            1.2 MB/s | 125 kB     00:00    
(2/15): dbus-libs-1.14.10-3.fc40.x86_64.rpm     1.3 MB/s | 156 kB     00:00    
(3/15): dnf5-5.2.2.0-1.fc41.x86_64.rpm          5.2 MB/s | 692 kB     00:00    
(4/15): libdnf5-cli-5.2.2.0-1.fc41.x86_64.rpm    10 MB/s | 306 kB     00:00    
(5/15): python3-dateutil-2.8.2-13.fc40.noarch.r  10 MB/s | 345 kB     00:00    
(6/15): libdnf5-5.2.2.0-1.fc41.x86_64.rpm        14 MB/s | 1.0 MB     00:00    
(7/15): python3-distro-1.9.0-3.fc40.noarch.rpm  2.5 MB/s |  45 kB     00:00    
(8/15): python3-dbus-1.3.2-6.fc40.x86_64.rpm    3.7 MB/s | 145 kB     00:00    
(9/15): python3-six-1.16.0-14.fc40.noarch.rpm   2.0 MB/s |  41 kB     00:00    
(10/15): python3-dnf-plugins-core-4.7.0-1.fc41.  10 MB/s | 302 kB     00:00    
(11/15): python3-systemd-235-9.fc40.x86_64.rpm  4.2 MB/s | 100 kB     00:00    
(12/15): dnf-data-4.20.0-1.fc41.noarch.rpm      1.8 MB/s |  39 kB     00:00    
(13/15): sdbus-cpp-1.5.0-2.fc41.x86_64.rpm      3.9 MB/s | 113 kB     00:00    
(14/15): libstdc++-14.1.1-4.fc41.x86_64.rpm      26 MB/s | 884 kB     00:00    
(15/15): python3-dnf-4.20.0-1.fc41.noarch.rpm    20 MB/s | 580 kB     00:00    
--------------------------------------------------------------------------------
Total                                            18 MB/s | 4.8 MB     00:00     
Running transaction check
Transaction check succeeded.
Running transaction test
Transaction test succeeded.
Running transaction
  Preparing        :                                                        1/1 
  Upgrading        : libstdc++-14.1.1-4.fc41.x86_64                        1/20 
  Installing       : fmt-10.2.1-4.fc41.x86_64                              2/20 
  Installing       : libdnf5-5.2.2.0-1.fc41.x86_64                         3/20 
warning: /etc/dnf/dnf.conf created as /etc/dnf/dnf.conf.rpmnew

  Installing       : libdnf5-cli-5.2.2.0-1.fc41.x86_64                     4/20 
  Upgrading        : dnf-data-4.20.0-1.fc41.noarch                         5/20 
  Upgrading        : python3-dnf-4.20.0-1.fc41.noarch                      6/20 
  Installing       : sdbus-cpp-1.5.0-2.fc41.x86_64                         7/20 
  Installing       : python3-systemd-235-9.fc40.x86_64                     8/20 
  Installing       : python3-six-1.16.0-14.fc40.noarch                     9/20 
  Installing       : python3-dateutil-1:2.8.2-13.fc40.noarch              10/20 
  Installing       : python3-distro-1.9.0-3.fc40.noarch                   11/20 
  Installing       : dbus-libs-1:1.14.10-3.fc40.x86_64                    12/20 
  Installing       : python3-dbus-1.3.2-6.fc40.x86_64                     13/20 
  Installing       : python3-dnf-plugins-core-4.7.0-1.fc41.noarch         14/20 
  Installing       : dnf5-5.2.2.0-1.fc41.x86_64                           15/20 
  Obsoleting       : yum-4.19.2-1.fc39.noarch                             16/20 
  Running scriptlet: dnf-4.19.2-1.fc39.noarch                             17/20 
  Obsoleting       : dnf-4.19.2-1.fc39.noarch                             17/20 
warning: directory /var/cache/dnf: remove failed: Device or resource busy

  Running scriptlet: dnf-4.19.2-1.fc39.noarch                             17/20 
  Cleanup          : python3-dnf-4.19.2-1.fc39.noarch                     18/20 
  Cleanup          : dnf-data-4.19.2-1.fc39.noarch                        19/20 
  Cleanup          : libstdc++-13.3.1-1.fc39.x86_64                       20/20 
  Running scriptlet: libstdc++-13.3.1-1.fc39.x86_64                       20/20 
  Verifying        : dbus-libs-1:1.14.10-3.fc40.x86_64                     1/20 
  Verifying        : dnf5-5.2.2.0-1.fc41.x86_64                            2/20 
  Verifying        : dnf-4.19.2-1.fc39.noarch                              3/20 
  Verifying        : yum-4.19.2-1.fc39.noarch                              4/20 
  Verifying        : fmt-10.2.1-4.fc41.x86_64                              5/20 
  Verifying        : libdnf5-5.2.2.0-1.fc41.x86_64                         6/20 
  Verifying        : libdnf5-cli-5.2.2.0-1.fc41.x86_64                     7/20 
  Verifying        : python3-dateutil-1:2.8.2-13.fc40.noarch               8/20 
  Verifying        : python3-dbus-1.3.2-6.fc40.x86_64                      9/20 
  Verifying        : python3-distro-1.9.0-3.fc40.noarch                   10/20 
  Verifying        : python3-dnf-plugins-core-4.7.0-1.fc41.noarch         11/20 
  Verifying        : python3-six-1.16.0-14.fc40.noarch                    12/20 
  Verifying        : python3-systemd-235-9.fc40.x86_64                    13/20 
  Verifying        : sdbus-cpp-1.5.0-2.fc41.x86_64                        14/20 
  Verifying        : dnf-data-4.20.0-1.fc41.noarch                        15/20 
  Verifying        : dnf-data-4.19.2-1.fc39.noarch                        16/20 
  Verifying        : libstdc++-14.1.1-4.fc41.x86_64                       17/20 
  Verifying        : libstdc++-13.3.1-1.fc39.x86_64                       18/20 
  Verifying        : python3-dnf-4.20.0-1.fc41.noarch                     19/20 
  Verifying        : python3-dnf-4.19.2-1.fc39.noarch                     20/20 

Upgraded:
  dnf-data-4.20.0-1.fc41.noarch           libstdc++-14.1.1-4.fc41.x86_64       
  python3-dnf-4.20.0-1.fc41.noarch       
Installed:
  dbus-libs-1:1.14.10-3.fc40.x86_64                                             
  dnf5-5.2.2.0-1.fc41.x86_64                                                    
  fmt-10.2.1-4.fc41.x86_64                                                      
  libdnf5-5.2.2.0-1.fc41.x86_64                                                 
  libdnf5-cli-5.2.2.0-1.fc41.x86_64                                             
  python3-dateutil-1:2.8.2-13.fc40.noarch                                       
  python3-dbus-1.3.2-6.fc40.x86_64                                              
  python3-distro-1.9.0-3.fc40.noarch                                            
  python3-dnf-plugins-core-4.7.0-1.fc41.noarch                                  
  python3-six-1.16.0-14.fc40.noarch                                             
  python3-systemd-235-9.fc40.x86_64                                             
  sdbus-cpp-1.5.0-2.fc41.x86_64                                                 

Complete!
Finish(bootstrap): installing dnf tooling
Start(bootstrap): creating root cache
Finish(bootstrap): creating root cache
Finish(bootstrap): chroot init
Start: chroot init
INFO: mounting tmpfs at /var/lib/mock/fedora-39-x86_64-1717081834.800473/root.
INFO: calling preinit hooks
INFO: enabled root cache
INFO: enabled package manager cache
Start: cleaning package manager metadata
Finish: cleaning package manager metadata
INFO: enabled HW Info plugin
INFO: Package manager dnf detected and used (direct choice)
INFO: Buildroot is handled by package management downloaded with a bootstrap image:
  rpm-4.19.1.1-1.fc39.x86_64
  rpm-sequoia-1.6.0-1.fc39.x86_64
  python3-dnf-4.20.0-1.fc41.noarch
  python3-dnf-plugins-core-4.7.0-1.fc41.noarch
  dnf5-5.2.2.0-1.fc41.x86_64
Start: installing minimal buildroot with dnf
No matches found for the following disable plugin patterns: local, spacewalk, versionlock
Copr repository                                  56 MB/s |  19 MB     00:00    
Additional repo http_kojipkgs_fedoraproject_org  67 MB/s |  75 MB     00:01    
fedora                                           31 MB/s |  89 MB     00:02    
updates                                          18 MB/s |  38 MB     00:02    
Last metadata expiration check: 0:00:03 ago on Thu May 30 15:12:29 2024.
Dependencies resolved.
============================================================================================================================================
 Package                             Arch    Version                    Repository                                                      Size
============================================================================================================================================
Installing group/module packages:
 bash                                x86_64  5.2.26-3.fc40              http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch  1.8 M
 bzip2                               x86_64  1.0.8-18.fc40              http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   52 k
 coreutils                           x86_64  9.5-1.fc41                 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch  1.1 M
 cpio                                x86_64  2.15-1.fc40                http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch  285 k
 diffutils                           x86_64  3.10-5.fc40                http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch  397 k
 fedora-release-common               noarch  41-0.13                    http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   22 k
 findutils                           x86_64  1:4.9.0-8.fc40             http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch  482 k
 gawk                                x86_64  5.3.0-3.fc40               http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch  1.1 M
 glibc-minimal-langpack              x86_64  2.39.9000-18.fc41          http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch  112 k
 grep                                x86_64  3.11-8.fc41                http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch  289 k
 gzip                                x86_64  1.13-1.fc40                http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch  164 k
 info                                x86_64  7.1-2.fc40                 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch  182 k
 patch                               x86_64  2.7.6-24.fc40              http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch  131 k
 redhat-rpm-config                   noarch  291-1.fc41                 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   76 k
 rpm-build                           x86_64  4.19.91-4.fc41             http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   75 k
 sed                                 x86_64  4.9-1.fc40                 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch  309 k
 shadow-utils                        x86_64  2:4.15.1-5.fc41            http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch  1.3 M
 tar                                 x86_64  2:1.35-3.fc40              http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch  847 k
 unzip                               x86_64  6.0-63.fc40                http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch  185 k
 util-linux                          x86_64  2.40.1-1.fc41              http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch  1.2 M
 which                               x86_64  2.21-41.fc40               http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   41 k
 xz                                  x86_64  1:5.4.6-3.fc41             http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch  532 k
Installing dependencies:
 add-determinism-nopython            x86_64  0.2.0-9.fc41               http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch  891 k
 alternatives                        x86_64  1.27-1.fc41                http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   41 k
 ansible-srpm-macros                 noarch  1-15.fc41                  http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   21 k
 audit-libs                          x86_64  4.0.1-2.fc41               http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch  125 k
 authselect                          x86_64  1.5.0-5.fc41               http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch  141 k
 authselect-libs                     x86_64  1.5.0-5.fc41               http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch  205 k
 basesystem                          noarch  11-20.fc40                 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch  7.2 k
 binutils                            x86_64  2.42.50-11.fc41            http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch  6.4 M
 binutils-gold                       x86_64  2.42.50-11.fc41            http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch  783 k
 build-reproducibility-srpm-macros   noarch  0.2.0-9.fc41               http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch  9.1 k
 bzip2-libs                          x86_64  1.0.8-18.fc40              http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   41 k
 ca-certificates                     noarch  2023.2.62_v7.0.401-6.fc40  http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch  862 k
 coreutils-common                    x86_64  9.5-1.fc41                 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch  2.1 M
 cracklib                            x86_64  2.9.11-5.fc40              http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   82 k
 crypto-policies                     noarch  20240521-1.gitf71d135.fc41 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   65 k
 curl                                x86_64  8.8.0-1.fc41               http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch  302 k
 cyrus-sasl-lib                      x86_64  2.1.28-22.fc41             http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch  793 k
 debugedit                           x86_64  5.0-16.fc41                http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   80 k
 dwz                                 x86_64  0.15-6.fc40                http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch  138 k
 ed                                  x86_64  1.20.2-1.fc41              http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   82 k
 efi-srpm-macros                     noarch  5-11.fc40                  http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   22 k
 elfutils                            x86_64  0.191-7.fc41               http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch  524 k
 elfutils-debuginfod-client          x86_64  0.191-7.fc41               http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   38 k
 elfutils-default-yama-scope         noarch  0.191-7.fc41               http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   13 k
 elfutils-libelf                     x86_64  0.191-7.fc41               http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch  208 k
 elfutils-libs                       x86_64  0.191-7.fc41               http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch  258 k
 fedora-gpg-keys                     noarch  41-0.2                     http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch  122 k
 fedora-release                      noarch  41-0.13                    http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   11 k
 fedora-release-identity-basic       noarch  41-0.13                    http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   12 k
 fedora-repos                        noarch  41-0.2                     http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch  9.3 k
 fedora-repos-rawhide                noarch  41-0.2                     http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch  8.9 k
 file                                x86_64  5.45-5.fc41                http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   49 k
 file-libs                           x86_64  5.45-5.fc41                http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch  763 k
 filesystem                          x86_64  3.18-9.fc41                http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch  1.1 M
 fonts-srpm-macros                   noarch  1:2.0.5-14.fc40            http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   27 k
 forge-srpm-macros                   noarch  0.3.1-1.fc41               http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   19 k
 fpc-srpm-macros                     noarch  1.3-12.fc40                http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch  7.8 k
 gdb-minimal                         x86_64  14.2-9.fc41                copr_base                                                      4.3 M
 gdbm                                x86_64  1:1.23-6.fc40              http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch  147 k
 gdbm-libs                           x86_64  1:1.23-6.fc40              http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   56 k
 ghc-srpm-macros                     noarch  1.9.1-1.fc41               http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch  9.0 k
 glibc                               x86_64  2.39.9000-18.fc41          http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch  2.2 M
 glibc-common                        x86_64  2.39.9000-18.fc41          http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch  394 k
 glibc-gconv-extra                   x86_64  2.39.9000-18.fc41          http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch  1.6 M
 gmp                                 x86_64  1:6.3.0-1.fc41             http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch  317 k
 gnat-srpm-macros                    noarch  6-5.fc40                   http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch  8.8 k
 go-srpm-macros                      noarch  3.6.0-1.fc41               http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   28 k
 jansson                             x86_64  2.13.1-9.fc40              http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   44 k
 kernel-srpm-macros                  noarch  1.0-23.fc41                http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch  9.8 k
 keyutils-libs                       x86_64  1.6.3-3.fc40               http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   31 k
 krb5-libs                           x86_64  1.21.2-5.fc40              http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch  751 k
 libacl                              x86_64  2.3.2-1.fc40               http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   24 k
 libarchive                          x86_64  3.7.4-1.fc41               http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch  408 k
 libattr                             x86_64  2.5.2-3.fc40               http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   18 k
 libblkid                            x86_64  2.40.1-1.fc41              http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch  124 k
 libbrotli                           x86_64  1.1.0-3.fc40               http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch  338 k
 libcap                              x86_64  2.70-1.fc41                http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   86 k
 libcap-ng                           x86_64  0.8.5-1.fc41               http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   32 k
 libcom_err                          x86_64  1.47.0-5.fc40              http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   25 k
 libcurl                             x86_64  8.8.0-1.fc41               http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch  355 k
 libeconf                            x86_64  0.6.2-2.fc41               http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   32 k
 libevent                            x86_64  2.1.12-13.fc41             http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch  257 k
 libfdisk                            x86_64  2.40.1-1.fc41              http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch  159 k
 libffi                              x86_64  3.4.6-1.fc41               http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   40 k
 libgcc                              x86_64  14.1.1-4.fc41              http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch  128 k
 libgomp                             x86_64  14.1.1-4.fc41              http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch  349 k
 libidn2                             x86_64  2.3.7-1.fc40               http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch  112 k
 libmount                            x86_64  2.40.1-1.fc41              http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch  155 k
 libnghttp2                          x86_64  1.62.0-1.fc41              http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   76 k
 libnsl2                             x86_64  2.0.1-1.fc40               http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   30 k
 libpkgconf                          x86_64  2.1.1-1.fc41               http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   38 k
 libpsl                              x86_64  0.21.5-3.fc40              http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   64 k
 libpwquality                        x86_64  1.4.5-9.fc40               http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch  108 k
 libselinux                          x86_64  3.6-4.fc40                 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   88 k
 libsemanage                         x86_64  3.6-3.fc40                 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch  116 k
 libsepol                            x86_64  3.6-3.fc40                 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch  340 k
 libsmartcols                        x86_64  2.40.1-1.fc41              http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   83 k
 libssh                              x86_64  0.10.6-6.fc41              http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch  212 k
 libssh-config                       noarch  0.10.6-6.fc41              http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch  9.1 k
 libstdc++                           x86_64  14.1.1-4.fc41              http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch  884 k
 libtasn1                            x86_64  4.19.0-6.fc40              http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   74 k
 libtirpc                            x86_64  1.3.4-1.rc3.fc41           http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   92 k
 libtool-ltdl                        x86_64  2.4.7-10.fc40              http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   36 k
 libunistring                        x86_64  1.1-7.fc41                 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch  545 k
 libutempter                         x86_64  1.2.1-13.fc40              http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   26 k
 libuuid                             x86_64  2.40.1-1.fc41              http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   28 k
 libverto                            x86_64  0.3.2-8.fc40               http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   21 k
 libxcrypt                           x86_64  4.4.36-5.fc40              http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch  118 k
 libxml2                             x86_64  2.12.7-1.fc41              http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch  685 k
 libzstd                             x86_64  1.5.6-1.fc41               http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch  309 k
 lua-libs                            x86_64  5.4.6-5.fc40               http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch  132 k
 lua-srpm-macros                     noarch  1-13.fc40                  http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch  8.7 k
 lz4-libs                            x86_64  1.9.4-6.fc40               http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   67 k
 mpfr                                x86_64  4.2.1-4.fc41               http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch  345 k
 ncurses-base                        noarch  6.4-12.20240127.fc40       http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   64 k
 ncurses-libs                        x86_64  6.4-12.20240127.fc40       http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch  332 k
 ocaml-srpm-macros                   noarch  10-1.fc41                  http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch  9.0 k
 openblas-srpm-macros                noarch  2-17.fc41                  http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch  7.7 k
 openldap                            x86_64  2.6.8-1.fc41               http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch  254 k
 openssl-libs                        x86_64  1:3.2.1-6.fc41             http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch  2.3 M
 p11-kit                             x86_64  0.25.3-4.fc40              http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch  476 k
 p11-kit-trust                       x86_64  0.25.3-4.fc40              http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch  132 k
 package-notes-srpm-macros           noarch  0.5-11.fc40                http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch  9.9 k
 pam                                 x86_64  1.6.1-3.fc41               http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch  517 k
 pam-libs                            x86_64  1.6.1-3.fc41               http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   57 k
 pcre2                               x86_64  10.43-2.fc41.1             http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch  242 k
 pcre2-syntax                        noarch  10.43-2.fc41.1             http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch  149 k
 perl-srpm-macros                    noarch  1-53.fc40                  http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch  8.4 k
 pkgconf                             x86_64  2.1.1-1.fc41               http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   44 k
 pkgconf-m4                          noarch  2.1.1-1.fc41               http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   14 k
 pkgconf-pkg-config                  x86_64  2.1.1-1.fc41               http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch  9.9 k
 popt                                x86_64  1.19-6.fc40                http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   60 k
 publicsuffix-list-dafsa             noarch  20240107-3.fc40            http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   58 k
 pyproject-srpm-macros               noarch  1.12.0-1.fc40              http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   14 k
 python-srpm-macros                  noarch  3.12-9.fc41                http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   24 k
 qt5-srpm-macros                     noarch  5.15.13-1.fc41             http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch  8.5 k
 qt6-srpm-macros                     noarch  6.7.1-1.fc41               http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch  8.9 k
 readline                            x86_64  8.2-8.fc40                 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch  213 k
 rpm                                 x86_64  4.19.91-4.fc41             http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch  520 k
 rpm-build-libs                      x86_64  4.19.91-4.fc41             http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   98 k
 rpm-libs                            x86_64  4.19.91-4.fc41             http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch  308 k
 rpm-sequoia                         x86_64  1.6.0-3.fc41               http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch  846 k
 rust-srpm-macros                    noarch  26.3-1.fc41                http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   13 k
 setup                               noarch  2.15.0-3.fc41              http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch  148 k
 sqlite-libs                         x86_64  3.45.3-1.fc41              http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch  705 k
 systemd-libs                        x86_64  256~rc3-3.fc41             http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch  727 k
 util-linux-core                     x86_64  2.40.1-1.fc41              http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch  520 k
 xxhash-libs                         x86_64  0.8.2-2.fc40               http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   37 k
 xz-libs                             x86_64  1:5.4.6-3.fc41             http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch  110 k
 zig-srpm-macros                     noarch  1-2.fc40                   http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch  8.0 k
 zip                                 x86_64  3.0-40.fc40                http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch  265 k
 zlib-ng-compat                      x86_64  2.1.6-4.fc41               http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   77 k
 zstd                                x86_64  1.5.6-1.fc41               http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch  479 k
Installing Groups:
 Buildsystem building group                                                                                                                 

Transaction Summary
============================================================================================================================================
Install  155 Packages

Total download size: 53 M
Installed size: 182 M
Downloading Packages:
(1/155): alternatives-1.27-1.fc41.x86_64.rpm    514 kB/s |  41 kB     00:00    
(2/155): ansible-srpm-macros-1-15.fc41.noarch.r 880 kB/s |  21 kB     00:00    
(3/155): add-determinism-nopython-0.2.0-9.fc41. 7.5 MB/s | 891 kB     00:00    
(4/155): gdb-minimal-14.2-9.fc41.x86_64.rpm      32 MB/s | 4.3 MB     00:00    
(5/155): authselect-1.5.0-5.fc41.x86_64.rpm     6.6 MB/s | 141 kB     00:00    
(6/155): audit-libs-4.0.1-2.fc41.x86_64.rpm     2.8 MB/s | 125 kB     00:00    
(7/155): authselect-libs-1.5.0-5.fc41.x86_64.rp 9.0 MB/s | 205 kB     00:00    
(8/155): basesystem-11-20.fc40.noarch.rpm       167 kB/s | 7.2 kB     00:00    
(9/155): bash-5.2.26-3.fc40.x86_64.rpm           19 MB/s | 1.8 MB     00:00    
(10/155): binutils-2.42.50-11.fc41.x86_64.rpm    58 MB/s | 6.4 MB     00:00    
(11/155): build-reproducibility-srpm-macros-0.2 254 kB/s | 9.1 kB     00:00    
(12/155): bzip2-1.0.8-18.fc40.x86_64.rpm        1.7 MB/s |  52 kB     00:00    
(13/155): bzip2-libs-1.0.8-18.fc40.x86_64.rpm   1.3 MB/s |  41 kB     00:00    
(14/155): coreutils-9.5-1.fc41.x86_64.rpm        30 MB/s | 1.1 MB     00:00    
(15/155): ca-certificates-2023.2.62_v7.0.401-6.  16 MB/s | 862 kB     00:00    
(16/155): cpio-2.15-1.fc40.x86_64.rpm            12 MB/s | 285 kB     00:00    
(17/155): cracklib-2.9.11-5.fc40.x86_64.rpm     3.5 MB/s |  82 kB     00:00    
(18/155): crypto-policies-20240521-1.gitf71d135 3.0 MB/s |  65 kB     00:00    
(19/155): coreutils-common-9.5-1.fc41.x86_64.rp  25 MB/s | 2.1 MB     00:00    
(20/155): curl-8.8.0-1.fc41.x86_64.rpm           12 MB/s | 302 kB     00:00    
(21/155): binutils-gold-2.42.50-11.fc41.x86_64. 2.8 MB/s | 783 kB     00:00    
(22/155): cyrus-sasl-lib-2.1.28-22.fc41.x86_64.  25 MB/s | 793 kB     00:00    
(23/155): debugedit-5.0-16.fc41.x86_64.rpm      3.3 MB/s |  80 kB     00:00    
(24/155): diffutils-3.10-5.fc40.x86_64.rpm       17 MB/s | 397 kB     00:00    
(25/155): dwz-0.15-6.fc40.x86_64.rpm            6.4 MB/s | 138 kB     00:00    
(26/155): elfutils-0.191-7.fc41.x86_64.rpm       22 MB/s | 524 kB     00:00    
(27/155): ed-1.20.2-1.fc41.x86_64.rpm           2.1 MB/s |  82 kB     00:00    
(28/155): efi-srpm-macros-5-11.fc40.noarch.rpm  850 kB/s |  22 kB     00:00    
(29/155): elfutils-default-yama-scope-0.191-7.f 692 kB/s |  13 kB     00:00    
(30/155): elfutils-debuginfod-client-0.191-7.fc 1.7 MB/s |  38 kB     00:00    
(31/155): elfutils-libelf-0.191-7.fc41.x86_64.r 5.6 MB/s | 208 kB     00:00    
(32/155): fedora-gpg-keys-41-0.2.noarch.rpm     6.3 MB/s | 122 kB     00:00    
(33/155): fedora-release-41-0.13.noarch.rpm     536 kB/s |  11 kB     00:00    
(34/155): fedora-release-common-41-0.13.noarch. 882 kB/s |  22 kB     00:00    
(35/155): fedora-release-identity-basic-41-0.13 585 kB/s |  12 kB     00:00    
(36/155): fedora-repos-41-0.2.noarch.rpm        553 kB/s | 9.3 kB     00:00    
(37/155): elfutils-libs-0.191-7.fc41.x86_64.rpm 3.8 MB/s | 258 kB     00:00    
(38/155): fedora-repos-rawhide-41-0.2.noarch.rp 423 kB/s | 8.9 kB     00:00    
(39/155): file-5.45-5.fc41.x86_64.rpm           2.6 MB/s |  49 kB     00:00    
(40/155): filesystem-3.18-9.fc41.x86_64.rpm      26 MB/s | 1.1 MB     00:00    
(41/155): findutils-4.9.0-8.fc40.x86_64.rpm      12 MB/s | 482 kB     00:00    
(42/155): fonts-srpm-macros-2.0.5-14.fc40.noarc 1.0 MB/s |  27 kB     00:00    
(43/155): forge-srpm-macros-0.3.1-1.fc41.noarch 716 kB/s |  19 kB     00:00    
(44/155): fpc-srpm-macros-1.3-12.fc40.noarch.rp 353 kB/s | 7.8 kB     00:00    
(45/155): gdbm-1.23-6.fc40.x86_64.rpm           5.6 MB/s | 147 kB     00:00    
(46/155): gawk-5.3.0-3.fc40.x86_64.rpm           21 MB/s | 1.1 MB     00:00    
(47/155): ghc-srpm-macros-1.9.1-1.fc41.noarch.r 477 kB/s | 9.0 kB     00:00    
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(51/155): glibc-minimal-langpack-2.39.9000-18.f 4.6 MB/s | 112 kB     00:00    
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(53/155): gnat-srpm-macros-6-5.fc40.noarch.rpm  364 kB/s | 8.8 kB     00:00    
(54/155): glibc-2.39.9000-18.fc41.x86_64.rpm     22 MB/s | 2.2 MB     00:00    
(55/155): go-srpm-macros-3.6.0-1.fc41.noarch.rp 1.2 MB/s |  28 kB     00:00    
(56/155): grep-3.11-8.fc41.x86_64.rpm            11 MB/s | 289 kB     00:00    
(57/155): gzip-1.13-1.fc40.x86_64.rpm           6.4 MB/s | 164 kB     00:00    
(58/155): info-7.1-2.fc40.x86_64.rpm            7.3 MB/s | 182 kB     00:00    
(59/155): kernel-srpm-macros-1.0-23.fc41.noarch 560 kB/s | 9.8 kB     00:00    
(60/155): jansson-2.13.1-9.fc40.x86_64.rpm      1.6 MB/s |  44 kB     00:00    
(61/155): keyutils-libs-1.6.3-3.fc40.x86_64.rpm 1.4 MB/s |  31 kB     00:00    
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(65/155): glibc-gconv-extra-2.39.9000-18.fc41.x 7.0 MB/s | 1.6 MB     00:00    
(66/155): libattr-2.5.2-3.fc40.x86_64.rpm       724 kB/s |  18 kB     00:00    
(67/155): libblkid-2.40.1-1.fc41.x86_64.rpm     6.5 MB/s | 124 kB     00:00    
(68/155): libcap-2.70-1.fc41.x86_64.rpm         4.2 MB/s |  86 kB     00:00    
(69/155): libbrotli-1.1.0-3.fc40.x86_64.rpm      14 MB/s | 338 kB     00:00    
(70/155): libcap-ng-0.8.5-1.fc41.x86_64.rpm     1.5 MB/s |  32 kB     00:00    
(71/155): libcurl-8.8.0-1.fc41.x86_64.rpm        17 MB/s | 355 kB     00:00    
(72/155): libcom_err-1.47.0-5.fc40.x86_64.rpm   1.0 MB/s |  25 kB     00:00    
(73/155): libeconf-0.6.2-2.fc41.x86_64.rpm      1.5 MB/s |  32 kB     00:00    
(74/155): libevent-2.1.12-13.fc41.x86_64.rpm     11 MB/s | 257 kB     00:00    
(75/155): libfdisk-2.40.1-1.fc41.x86_64.rpm     6.6 MB/s | 159 kB     00:00    
(76/155): libffi-3.4.6-1.fc41.x86_64.rpm        1.8 MB/s |  40 kB     00:00    
(77/155): libgcc-14.1.1-4.fc41.x86_64.rpm       5.7 MB/s | 128 kB     00:00    
(78/155): libgomp-14.1.1-4.fc41.x86_64.rpm       13 MB/s | 349 kB     00:00    
(79/155): libidn2-2.3.7-1.fc40.x86_64.rpm       3.6 MB/s | 112 kB     00:00    
(80/155): libnghttp2-1.62.0-1.fc41.x86_64.rpm   4.2 MB/s |  76 kB     00:00    
(81/155): libmount-2.40.1-1.fc41.x86_64.rpm     5.9 MB/s | 155 kB     00:00    
(82/155): libnsl2-2.0.1-1.fc40.x86_64.rpm       1.4 MB/s |  30 kB     00:00    
(83/155): libpkgconf-2.1.1-1.fc41.x86_64.rpm    1.8 MB/s |  38 kB     00:00    
(84/155): libpsl-0.21.5-3.fc40.x86_64.rpm       3.1 MB/s |  64 kB     00:00    
(85/155): libpwquality-1.4.5-9.fc40.x86_64.rpm  3.8 MB/s | 108 kB     00:00    
(86/155): libselinux-3.6-4.fc40.x86_64.rpm      1.3 MB/s |  88 kB     00:00    
(87/155): libsemanage-3.6-3.fc40.x86_64.rpm     1.8 MB/s | 116 kB     00:00    
(88/155): libssh-0.10.6-6.fc41.x86_64.rpm       8.5 MB/s | 212 kB     00:00    
(89/155): libsmartcols-2.40.1-1.fc41.x86_64.rpm 3.0 MB/s |  83 kB     00:00    
(90/155): libsepol-3.6-3.fc40.x86_64.rpm        4.2 MB/s | 340 kB     00:00    
(91/155): libssh-config-0.10.6-6.fc41.noarch.rp 430 kB/s | 9.1 kB     00:00    
(92/155): libtasn1-4.19.0-6.fc40.x86_64.rpm     2.6 MB/s |  74 kB     00:00    
(93/155): libtirpc-1.3.4-1.rc3.fc41.x86_64.rpm  3.2 MB/s |  92 kB     00:00    
(94/155): libtool-ltdl-2.4.7-10.fc40.x86_64.rpm 1.8 MB/s |  36 kB     00:00    
(95/155): libstdc++-14.1.1-4.fc41.x86_64.rpm     16 MB/s | 884 kB     00:00    
(96/155): libutempter-1.2.1-13.fc40.x86_64.rpm  1.1 MB/s |  26 kB     00:00    
(97/155): libunistring-1.1-7.fc41.x86_64.rpm     19 MB/s | 545 kB     00:00    
(98/155): libuuid-2.40.1-1.fc41.x86_64.rpm      1.0 MB/s |  28 kB     00:00    
(99/155): libverto-0.3.2-8.fc40.x86_64.rpm      990 kB/s |  21 kB     00:00    
(100/155): libxcrypt-4.4.36-5.fc40.x86_64.rpm   6.2 MB/s | 118 kB     00:00    
(101/155): lua-libs-5.4.6-5.fc40.x86_64.rpm     6.5 MB/s | 132 kB     00:00    
(102/155): libzstd-1.5.6-1.fc41.x86_64.rpm       12 MB/s | 309 kB     00:00    
(103/155): lua-srpm-macros-1-13.fc40.noarch.rpm 399 kB/s | 8.7 kB     00:00    
(104/155): lz4-libs-1.9.4-6.fc40.x86_64.rpm     3.1 MB/s |  67 kB     00:00    
(105/155): ncurses-base-6.4-12.20240127.fc40.no 3.1 MB/s |  64 kB     00:00    
(106/155): mpfr-4.2.1-4.fc41.x86_64.rpm          12 MB/s | 345 kB     00:00    
(107/155): libxml2-2.12.7-1.fc41.x86_64.rpm     7.9 MB/s | 685 kB     00:00    
(108/155): ocaml-srpm-macros-10-1.fc41.noarch.r 515 kB/s | 9.0 kB     00:00    
(109/155): ncurses-libs-6.4-12.20240127.fc40.x8  13 MB/s | 332 kB     00:00    
(110/155): openblas-srpm-macros-2-17.fc41.noarc 364 kB/s | 7.7 kB     00:00    
(111/155): openldap-2.6.8-1.fc41.x86_64.rpm     8.3 MB/s | 254 kB     00:00    
(112/155): openssl-libs-3.2.1-6.fc41.x86_64.rpm  46 MB/s | 2.3 MB     00:00    
(113/155): p11-kit-trust-0.25.3-4.fc40.x86_64.r 5.1 MB/s | 132 kB     00:00    
(114/155): p11-kit-0.25.3-4.fc40.x86_64.rpm     7.1 MB/s | 476 kB     00:00    
(115/155): package-notes-srpm-macros-0.5-11.fc4 467 kB/s | 9.9 kB     00:00    
(116/155): pam-1.6.1-3.fc41.x86_64.rpm           22 MB/s | 517 kB     00:00    
(117/155): patch-2.7.6-24.fc40.x86_64.rpm       7.0 MB/s | 131 kB     00:00    
(118/155): pam-libs-1.6.1-3.fc41.x86_64.rpm     2.5 MB/s |  57 kB     00:00    
(119/155): perl-srpm-macros-1-53.fc40.noarch.rp 417 kB/s | 8.4 kB     00:00    
(120/155): pcre2-syntax-10.43-2.fc41.1.noarch.r 6.8 MB/s | 149 kB     00:00    
(121/155): pcre2-10.43-2.fc41.1.x86_64.rpm      6.6 MB/s | 242 kB     00:00    
(122/155): pkgconf-2.1.1-1.fc41.x86_64.rpm      2.3 MB/s |  44 kB     00:00    
(123/155): pkgconf-m4-2.1.1-1.fc41.noarch.rpm   746 kB/s |  14 kB     00:00    
(124/155): pkgconf-pkg-config-2.1.1-1.fc41.x86_ 529 kB/s | 9.9 kB     00:00    
(125/155): popt-1.19-6.fc40.x86_64.rpm          3.0 MB/s |  60 kB     00:00    
(126/155): pyproject-srpm-macros-1.12.0-1.fc40. 718 kB/s |  14 kB     00:00    
(127/155): publicsuffix-list-dafsa-20240107-3.f 2.8 MB/s |  58 kB     00:00    
(128/155): python-srpm-macros-3.12-9.fc41.noarc 1.1 MB/s |  24 kB     00:00    
(129/155): qt5-srpm-macros-5.15.13-1.fc41.noarc 436 kB/s | 8.5 kB     00:00    
(130/155): qt6-srpm-macros-6.7.1-1.fc41.noarch. 448 kB/s | 8.9 kB     00:00    
(131/155): redhat-rpm-config-291-1.fc41.noarch. 3.7 MB/s |  76 kB     00:00    
(132/155): readline-8.2-8.fc40.x86_64.rpm       8.9 MB/s | 213 kB     00:00    
(133/155): rpm-build-4.19.91-4.fc41.x86_64.rpm  3.2 MB/s |  75 kB     00:00    
(134/155): rpm-build-libs-4.19.91-4.fc41.x86_64 4.7 MB/s |  98 kB     00:00    
(135/155): rpm-4.19.91-4.fc41.x86_64.rpm        8.5 MB/s | 520 kB     00:00    
(136/155): rpm-libs-4.19.91-4.fc41.x86_64.rpm    12 MB/s | 308 kB     00:00    
(137/155): rust-srpm-macros-26.3-1.fc41.noarch. 631 kB/s |  13 kB     00:00    
(138/155): rpm-sequoia-1.6.0-3.fc41.x86_64.rpm   20 MB/s | 846 kB     00:00    
(139/155): setup-2.15.0-3.fc41.noarch.rpm       6.4 MB/s | 148 kB     00:00    
(140/155): sed-4.9-1.fc40.x86_64.rpm            7.1 MB/s | 309 kB     00:00    
(141/155): shadow-utils-4.15.1-5.fc41.x86_64.rp  33 MB/s | 1.3 MB     00:00    
(142/155): sqlite-libs-3.45.3-1.fc41.x86_64.rpm  18 MB/s | 705 kB     00:00    
(143/155): tar-1.35-3.fc40.x86_64.rpm            24 MB/s | 847 kB     00:00    
(144/155): unzip-6.0-63.fc40.x86_64.rpm         7.4 MB/s | 185 kB     00:00    
(145/155): systemd-libs-256~rc3-3.fc41.x86_64.r 9.4 MB/s | 727 kB     00:00    
(146/155): util-linux-core-2.40.1-1.fc41.x86_64  14 MB/s | 520 kB     00:00    
(147/155): which-2.21-41.fc40.x86_64.rpm        1.6 MB/s |  41 kB     00:00    
(148/155): util-linux-2.40.1-1.fc41.x86_64.rpm   21 MB/s | 1.2 MB     00:00    
(149/155): xxhash-libs-0.8.2-2.fc40.x86_64.rpm  1.6 MB/s |  37 kB     00:00    
(150/155): xz-libs-5.4.6-3.fc41.x86_64.rpm      4.3 MB/s | 110 kB     00:00    
(151/155): zig-srpm-macros-1-2.fc40.noarch.rpm  429 kB/s | 8.0 kB     00:00    
(152/155): xz-5.4.6-3.fc41.x86_64.rpm            13 MB/s | 532 kB     00:00    
(153/155): zlib-ng-compat-2.1.6-4.fc41.x86_64.r 4.2 MB/s |  77 kB     00:00    
(154/155): zip-3.0-40.fc40.x86_64.rpm           9.9 MB/s | 265 kB     00:00    
(155/155): zstd-1.5.6-1.fc41.x86_64.rpm         9.2 MB/s | 479 kB     00:00    
--------------------------------------------------------------------------------
Total                                            28 MB/s |  53 MB     00:01     
Running transaction check
Transaction check succeeded.
Running transaction test
Transaction test succeeded.
Running transaction
  Running scriptlet: filesystem-3.18-9.fc41.x86_64                          1/1 
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warning: /etc/hosts created as /etc/hosts.rpmnew

  Running scriptlet: setup-2.15.0-3.fc41.noarch                           9/155 
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  Running scriptlet: p11-kit-trust-0.25.3-4.fc40.x86_64                  98/155 
  Installing       : libgomp-14.1.1-4.fc41.x86_64                        99/155 
  Installing       : libnghttp2-1.62.0-1.fc41.x86_64                    100/155 
  Installing       : libpkgconf-2.1.1-1.fc41.x86_64                     101/155 
  Installing       : pkgconf-2.1.1-1.fc41.x86_64                        102/155 
  Installing       : pkgconf-pkg-config-2.1.1-1.fc41.x86_64             103/155 
  Installing       : libtool-ltdl-2.4.7-10.fc40.x86_64                  104/155 
  Installing       : libverto-0.3.2-8.fc40.x86_64                       105/155 
  Installing       : xxhash-libs-0.8.2-2.fc40.x86_64                    106/155 
  Installing       : libssh-config-0.10.6-6.fc41.noarch                 107/155 
  Installing       : kernel-srpm-macros-1.0-23.fc41.noarch              108/155 
  Installing       : gnat-srpm-macros-6-5.fc40.noarch                   109/155 
  Installing       : ghc-srpm-macros-1.9.1-1.fc41.noarch                110/155 
  Installing       : fpc-srpm-macros-1.3-12.fc40.noarch                 111/155 
  Installing       : coreutils-common-9.5-1.fc41.x86_64                 112/155 
  Installing       : openssl-libs-1:3.2.1-6.fc41.x86_64                 113/155 
  Installing       : coreutils-9.5-1.fc41.x86_64                        114/155 
  Running scriptlet: ca-certificates-2023.2.62_v7.0.401-6.fc40.noarch   115/155 
  Installing       : ca-certificates-2023.2.62_v7.0.401-6.fc40.noarch   115/155 
  Running scriptlet: ca-certificates-2023.2.62_v7.0.401-6.fc40.noarch   115/155 
  Installing       : krb5-libs-1.21.2-5.fc40.x86_64                     116/155 
  Installing       : libarchive-3.7.4-1.fc41.x86_64                     117/155 
  Installing       : libtirpc-1.3.4-1.rc3.fc41.x86_64                   118/155 
  Installing       : authselect-libs-1.5.0-5.fc41.x86_64                119/155 
  Installing       : gzip-1.13-1.fc40.x86_64                            120/155 
  Installing       : cracklib-2.9.11-5.fc40.x86_64                      121/155 
  Installing       : libpwquality-1.4.5-9.fc40.x86_64                   122/155 
  Installing       : authselect-1.5.0-5.fc41.x86_64                     123/155 
  Installing       : libnsl2-2.0.1-1.fc40.x86_64                        124/155 
  Installing       : pam-1.6.1-3.fc41.x86_64                            125/155 
  Installing       : libssh-0.10.6-6.fc41.x86_64                        126/155 
  Installing       : libevent-2.1.12-13.fc41.x86_64                     127/155 
  Installing       : openldap-2.6.8-1.fc41.x86_64                       128/155 
  Installing       : libcurl-8.8.0-1.fc41.x86_64                        129/155 
  Installing       : elfutils-libs-0.191-7.fc41.x86_64                  130/155 
  Installing       : elfutils-debuginfod-client-0.191-7.fc41.x86_64     131/155 
  Installing       : binutils-gold-2.42.50-11.fc41.x86_64               132/155 
  Running scriptlet: binutils-gold-2.42.50-11.fc41.x86_64               132/155 
  Installing       : binutils-2.42.50-11.fc41.x86_64                    133/155 
  Running scriptlet: binutils-2.42.50-11.fc41.x86_64                    133/155 
  Installing       : gdb-minimal-14.2-9.fc41.x86_64                     134/155 
  Installing       : elfutils-0.191-7.fc41.x86_64                       135/155 
  Installing       : debugedit-5.0-16.fc41.x86_64                       136/155 
  Installing       : curl-8.8.0-1.fc41.x86_64                           137/155 
  Installing       : rpm-sequoia-1.6.0-3.fc41.x86_64                    138/155 
  Installing       : rpm-libs-4.19.91-4.fc41.x86_64                     139/155 
  Running scriptlet: rpm-4.19.91-4.fc41.x86_64                          140/155 
  Installing       : rpm-4.19.91-4.fc41.x86_64                          140/155 
  Installing       : efi-srpm-macros-5-11.fc40.noarch                   141/155 
  Installing       : lua-srpm-macros-1-13.fc40.noarch                   142/155 
  Installing       : zig-srpm-macros-1-2.fc40.noarch                    143/155 
  Installing       : rpm-build-libs-4.19.91-4.fc41.x86_64               144/155 
  Installing       : ansible-srpm-macros-1-15.fc41.noarch               145/155 
  Installing       : fonts-srpm-macros-1:2.0.5-14.fc40.noarch           146/155 
  Installing       : forge-srpm-macros-0.3.1-1.fc41.noarch              147/155 
  Installing       : go-srpm-macros-3.6.0-1.fc41.noarch                 148/155 
  Installing       : python-srpm-macros-3.12-9.fc41.noarch              149/155 
  Installing       : redhat-rpm-config-291-1.fc41.noarch                150/155 
  Installing       : rpm-build-4.19.91-4.fc41.x86_64                    151/155 
  Installing       : pyproject-srpm-macros-1.12.0-1.fc40.noarch         152/155 
  Installing       : util-linux-2.40.1-1.fc41.x86_64                    153/155 
  Running scriptlet: util-linux-2.40.1-1.fc41.x86_64                    153/155 
  Installing       : which-2.21-41.fc40.x86_64                          154/155 
  Installing       : info-7.1-2.fc40.x86_64                             155/155 
  Running scriptlet: filesystem-3.18-9.fc41.x86_64                      155/155 
  Running scriptlet: ca-certificates-2023.2.62_v7.0.401-6.fc40.noarch   155/155 
  Running scriptlet: authselect-libs-1.5.0-5.fc41.x86_64                155/155 
  Running scriptlet: rpm-4.19.91-4.fc41.x86_64                          155/155 
  Running scriptlet: info-7.1-2.fc40.x86_64                             155/155 

Installed:
  add-determinism-nopython-0.2.0-9.fc41.x86_64                                  
  alternatives-1.27-1.fc41.x86_64                                               
  ansible-srpm-macros-1-15.fc41.noarch                                          
  audit-libs-4.0.1-2.fc41.x86_64                                                
  authselect-1.5.0-5.fc41.x86_64                                                
  authselect-libs-1.5.0-5.fc41.x86_64                                           
  basesystem-11-20.fc40.noarch                                                  
  bash-5.2.26-3.fc40.x86_64                                                     
  binutils-2.42.50-11.fc41.x86_64                                               
  binutils-gold-2.42.50-11.fc41.x86_64                                          
  build-reproducibility-srpm-macros-0.2.0-9.fc41.noarch                         
  bzip2-1.0.8-18.fc40.x86_64                                                    
  bzip2-libs-1.0.8-18.fc40.x86_64                                               
  ca-certificates-2023.2.62_v7.0.401-6.fc40.noarch                              
  coreutils-9.5-1.fc41.x86_64                                                   
  coreutils-common-9.5-1.fc41.x86_64                                            
  cpio-2.15-1.fc40.x86_64                                                       
  cracklib-2.9.11-5.fc40.x86_64                                                 
  crypto-policies-20240521-1.gitf71d135.fc41.noarch                             
  curl-8.8.0-1.fc41.x86_64                                                      
  cyrus-sasl-lib-2.1.28-22.fc41.x86_64                                          
  debugedit-5.0-16.fc41.x86_64                                                  
  diffutils-3.10-5.fc40.x86_64                                                  
  dwz-0.15-6.fc40.x86_64                                                        
  ed-1.20.2-1.fc41.x86_64                                                       
  efi-srpm-macros-5-11.fc40.noarch                                              
  elfutils-0.191-7.fc41.x86_64                                                  
  elfutils-debuginfod-client-0.191-7.fc41.x86_64                                
  elfutils-default-yama-scope-0.191-7.fc41.noarch                               
  elfutils-libelf-0.191-7.fc41.x86_64                                           
  elfutils-libs-0.191-7.fc41.x86_64                                             
  fedora-gpg-keys-41-0.2.noarch                                                 
  fedora-release-41-0.13.noarch                                                 
  fedora-release-common-41-0.13.noarch                                          
  fedora-release-identity-basic-41-0.13.noarch                                  
  fedora-repos-41-0.2.noarch                                                    
  fedora-repos-rawhide-41-0.2.noarch                                            
  file-5.45-5.fc41.x86_64                                                       
  file-libs-5.45-5.fc41.x86_64                                                  
  filesystem-3.18-9.fc41.x86_64                                                 
  findutils-1:4.9.0-8.fc40.x86_64                                               
  fonts-srpm-macros-1:2.0.5-14.fc40.noarch                                      
  forge-srpm-macros-0.3.1-1.fc41.noarch                                         
  fpc-srpm-macros-1.3-12.fc40.noarch                                            
  gawk-5.3.0-3.fc40.x86_64                                                      
  gdb-minimal-14.2-9.fc41.x86_64                                                
  gdbm-1:1.23-6.fc40.x86_64                                                     
  gdbm-libs-1:1.23-6.fc40.x86_64                                                
  ghc-srpm-macros-1.9.1-1.fc41.noarch                                           
  glibc-2.39.9000-18.fc41.x86_64                                                
  glibc-common-2.39.9000-18.fc41.x86_64                                         
  glibc-gconv-extra-2.39.9000-18.fc41.x86_64                                    
  glibc-minimal-langpack-2.39.9000-18.fc41.x86_64                               
  gmp-1:6.3.0-1.fc41.x86_64                                                     
  gnat-srpm-macros-6-5.fc40.noarch                                              
  go-srpm-macros-3.6.0-1.fc41.noarch                                            
  grep-3.11-8.fc41.x86_64                                                       
  gzip-1.13-1.fc40.x86_64                                                       
  info-7.1-2.fc40.x86_64                                                        
  jansson-2.13.1-9.fc40.x86_64                                                  
  kernel-srpm-macros-1.0-23.fc41.noarch                                         
  keyutils-libs-1.6.3-3.fc40.x86_64                                             
  krb5-libs-1.21.2-5.fc40.x86_64                                                
  libacl-2.3.2-1.fc40.x86_64                                                    
  libarchive-3.7.4-1.fc41.x86_64                                                
  libattr-2.5.2-3.fc40.x86_64                                                   
  libblkid-2.40.1-1.fc41.x86_64                                                 
  libbrotli-1.1.0-3.fc40.x86_64                                                 
  libcap-2.70-1.fc41.x86_64                                                     
  libcap-ng-0.8.5-1.fc41.x86_64                                                 
  libcom_err-1.47.0-5.fc40.x86_64                                               
  libcurl-8.8.0-1.fc41.x86_64                                                   
  libeconf-0.6.2-2.fc41.x86_64                                                  
  libevent-2.1.12-13.fc41.x86_64                                                
  libfdisk-2.40.1-1.fc41.x86_64                                                 
  libffi-3.4.6-1.fc41.x86_64                                                    
  libgcc-14.1.1-4.fc41.x86_64                                                   
  libgomp-14.1.1-4.fc41.x86_64                                                  
  libidn2-2.3.7-1.fc40.x86_64                                                   
  libmount-2.40.1-1.fc41.x86_64                                                 
  libnghttp2-1.62.0-1.fc41.x86_64                                               
  libnsl2-2.0.1-1.fc40.x86_64                                                   
  libpkgconf-2.1.1-1.fc41.x86_64                                                
  libpsl-0.21.5-3.fc40.x86_64                                                   
  libpwquality-1.4.5-9.fc40.x86_64                                              
  libselinux-3.6-4.fc40.x86_64                                                  
  libsemanage-3.6-3.fc40.x86_64                                                 
  libsepol-3.6-3.fc40.x86_64                                                    
  libsmartcols-2.40.1-1.fc41.x86_64                                             
  libssh-0.10.6-6.fc41.x86_64                                                   
  libssh-config-0.10.6-6.fc41.noarch                                            
  libstdc++-14.1.1-4.fc41.x86_64                                                
  libtasn1-4.19.0-6.fc40.x86_64                                                 
  libtirpc-1.3.4-1.rc3.fc41.x86_64                                              
  libtool-ltdl-2.4.7-10.fc40.x86_64                                             
  libunistring-1.1-7.fc41.x86_64                                                
  libutempter-1.2.1-13.fc40.x86_64                                              
  libuuid-2.40.1-1.fc41.x86_64                                                  
  libverto-0.3.2-8.fc40.x86_64                                                  
  libxcrypt-4.4.36-5.fc40.x86_64                                                
  libxml2-2.12.7-1.fc41.x86_64                                                  
  libzstd-1.5.6-1.fc41.x86_64                                                   
  lua-libs-5.4.6-5.fc40.x86_64                                                  
  lua-srpm-macros-1-13.fc40.noarch                                              
  lz4-libs-1.9.4-6.fc40.x86_64                                                  
  mpfr-4.2.1-4.fc41.x86_64                                                      
  ncurses-base-6.4-12.20240127.fc40.noarch                                      
  ncurses-libs-6.4-12.20240127.fc40.x86_64                                      
  ocaml-srpm-macros-10-1.fc41.noarch                                            
  openblas-srpm-macros-2-17.fc41.noarch                                         
  openldap-2.6.8-1.fc41.x86_64                                                  
  openssl-libs-1:3.2.1-6.fc41.x86_64                                            
  p11-kit-0.25.3-4.fc40.x86_64                                                  
  p11-kit-trust-0.25.3-4.fc40.x86_64                                            
  package-notes-srpm-macros-0.5-11.fc40.noarch                                  
  pam-1.6.1-3.fc41.x86_64                                                       
  pam-libs-1.6.1-3.fc41.x86_64                                                  
  patch-2.7.6-24.fc40.x86_64                                                    
  pcre2-10.43-2.fc41.1.x86_64                                                   
  pcre2-syntax-10.43-2.fc41.1.noarch                                            
  perl-srpm-macros-1-53.fc40.noarch                                             
  pkgconf-2.1.1-1.fc41.x86_64                                                   
  pkgconf-m4-2.1.1-1.fc41.noarch                                                
  pkgconf-pkg-config-2.1.1-1.fc41.x86_64                                        
  popt-1.19-6.fc40.x86_64                                                       
  publicsuffix-list-dafsa-20240107-3.fc40.noarch                                
  pyproject-srpm-macros-1.12.0-1.fc40.noarch                                    
  python-srpm-macros-3.12-9.fc41.noarch                                         
  qt5-srpm-macros-5.15.13-1.fc41.noarch                                         
  qt6-srpm-macros-6.7.1-1.fc41.noarch                                           
  readline-8.2-8.fc40.x86_64                                                    
  redhat-rpm-config-291-1.fc41.noarch                                           
  rpm-4.19.91-4.fc41.x86_64                                                     
  rpm-build-4.19.91-4.fc41.x86_64                                               
  rpm-build-libs-4.19.91-4.fc41.x86_64                                          
  rpm-libs-4.19.91-4.fc41.x86_64                                                
  rpm-sequoia-1.6.0-3.fc41.x86_64                                               
  rust-srpm-macros-26.3-1.fc41.noarch                                           
  sed-4.9-1.fc40.x86_64                                                         
  setup-2.15.0-3.fc41.noarch                                                    
  shadow-utils-2:4.15.1-5.fc41.x86_64                                           
  sqlite-libs-3.45.3-1.fc41.x86_64                                              
  systemd-libs-256~rc3-3.fc41.x86_64                                            
  tar-2:1.35-3.fc40.x86_64                                                      
  unzip-6.0-63.fc40.x86_64                                                      
  util-linux-2.40.1-1.fc41.x86_64                                               
  util-linux-core-2.40.1-1.fc41.x86_64                                          
  which-2.21-41.fc40.x86_64                                                     
  xxhash-libs-0.8.2-2.fc40.x86_64                                               
  xz-1:5.4.6-3.fc41.x86_64                                                      
  xz-libs-1:5.4.6-3.fc41.x86_64                                                 
  zig-srpm-macros-1-2.fc40.noarch                                               
  zip-3.0-40.fc40.x86_64                                                        
  zlib-ng-compat-2.1.6-4.fc41.x86_64                                            
  zstd-1.5.6-1.fc41.x86_64                                                      

Complete!
Finish: installing minimal buildroot with dnf
Start: creating root cache
Finish: creating root cache
Finish: chroot init
INFO: Installed packages:
INFO: add-determinism-nopython-0.2.0-9.fc41.x86_64
alternatives-1.27-1.fc41.x86_64
ansible-srpm-macros-1-15.fc41.noarch
audit-libs-4.0.1-2.fc41.x86_64
authselect-1.5.0-5.fc41.x86_64
authselect-libs-1.5.0-5.fc41.x86_64
basesystem-11-20.fc40.noarch
bash-5.2.26-3.fc40.x86_64
binutils-2.42.50-11.fc41.x86_64
binutils-gold-2.42.50-11.fc41.x86_64
build-reproducibility-srpm-macros-0.2.0-9.fc41.noarch
bzip2-1.0.8-18.fc40.x86_64
bzip2-libs-1.0.8-18.fc40.x86_64
ca-certificates-2023.2.62_v7.0.401-6.fc40.noarch
coreutils-9.5-1.fc41.x86_64
coreutils-common-9.5-1.fc41.x86_64
cpio-2.15-1.fc40.x86_64
cracklib-2.9.11-5.fc40.x86_64
crypto-policies-20240521-1.gitf71d135.fc41.noarch
curl-8.8.0-1.fc41.x86_64
cyrus-sasl-lib-2.1.28-22.fc41.x86_64
debugedit-5.0-16.fc41.x86_64
diffutils-3.10-5.fc40.x86_64
dwz-0.15-6.fc40.x86_64
ed-1.20.2-1.fc41.x86_64
efi-srpm-macros-5-11.fc40.noarch
elfutils-0.191-7.fc41.x86_64
elfutils-debuginfod-client-0.191-7.fc41.x86_64
elfutils-default-yama-scope-0.191-7.fc41.noarch
elfutils-libelf-0.191-7.fc41.x86_64
elfutils-libs-0.191-7.fc41.x86_64
fedora-gpg-keys-41-0.2.noarch
fedora-release-41-0.13.noarch
fedora-release-common-41-0.13.noarch
fedora-release-identity-basic-41-0.13.noarch
fedora-repos-41-0.2.noarch
fedora-repos-rawhide-41-0.2.noarch
file-5.45-5.fc41.x86_64
file-libs-5.45-5.fc41.x86_64
filesystem-3.18-9.fc41.x86_64
findutils-4.9.0-8.fc40.x86_64
fonts-srpm-macros-2.0.5-14.fc40.noarch
forge-srpm-macros-0.3.1-1.fc41.noarch
fpc-srpm-macros-1.3-12.fc40.noarch
gawk-5.3.0-3.fc40.x86_64
gdb-minimal-14.2-9.fc41.x86_64
gdbm-1.23-6.fc40.x86_64
gdbm-libs-1.23-6.fc40.x86_64
ghc-srpm-macros-1.9.1-1.fc41.noarch
glibc-2.39.9000-18.fc41.x86_64
glibc-common-2.39.9000-18.fc41.x86_64
glibc-gconv-extra-2.39.9000-18.fc41.x86_64
glibc-minimal-langpack-2.39.9000-18.fc41.x86_64
gmp-6.3.0-1.fc41.x86_64
gnat-srpm-macros-6-5.fc40.noarch
go-srpm-macros-3.6.0-1.fc41.noarch
grep-3.11-8.fc41.x86_64
gzip-1.13-1.fc40.x86_64
info-7.1-2.fc40.x86_64
jansson-2.13.1-9.fc40.x86_64
kernel-srpm-macros-1.0-23.fc41.noarch
keyutils-libs-1.6.3-3.fc40.x86_64
krb5-libs-1.21.2-5.fc40.x86_64
libacl-2.3.2-1.fc40.x86_64
libarchive-3.7.4-1.fc41.x86_64
libattr-2.5.2-3.fc40.x86_64
libblkid-2.40.1-1.fc41.x86_64
libbrotli-1.1.0-3.fc40.x86_64
libcap-2.70-1.fc41.x86_64
libcap-ng-0.8.5-1.fc41.x86_64
libcom_err-1.47.0-5.fc40.x86_64
libcurl-8.8.0-1.fc41.x86_64
libeconf-0.6.2-2.fc41.x86_64
libevent-2.1.12-13.fc41.x86_64
libfdisk-2.40.1-1.fc41.x86_64
libffi-3.4.6-1.fc41.x86_64
libgcc-14.1.1-4.fc41.x86_64
libgomp-14.1.1-4.fc41.x86_64
libidn2-2.3.7-1.fc40.x86_64
libmount-2.40.1-1.fc41.x86_64
libnghttp2-1.62.0-1.fc41.x86_64
libnsl2-2.0.1-1.fc40.x86_64
libpkgconf-2.1.1-1.fc41.x86_64
libpsl-0.21.5-3.fc40.x86_64
libpwquality-1.4.5-9.fc40.x86_64
libselinux-3.6-4.fc40.x86_64
libsemanage-3.6-3.fc40.x86_64
libsepol-3.6-3.fc40.x86_64
libsmartcols-2.40.1-1.fc41.x86_64
libssh-0.10.6-6.fc41.x86_64
libssh-config-0.10.6-6.fc41.noarch
libstdc++-14.1.1-4.fc41.x86_64
libtasn1-4.19.0-6.fc40.x86_64
libtirpc-1.3.4-1.rc3.fc41.x86_64
libtool-ltdl-2.4.7-10.fc40.x86_64
libunistring-1.1-7.fc41.x86_64
libutempter-1.2.1-13.fc40.x86_64
libuuid-2.40.1-1.fc41.x86_64
libverto-0.3.2-8.fc40.x86_64
libxcrypt-4.4.36-5.fc40.x86_64
libxml2-2.12.7-1.fc41.x86_64
libzstd-1.5.6-1.fc41.x86_64
lua-libs-5.4.6-5.fc40.x86_64
lua-srpm-macros-1-13.fc40.noarch
lz4-libs-1.9.4-6.fc40.x86_64
mpfr-4.2.1-4.fc41.x86_64
ncurses-base-6.4-12.20240127.fc40.noarch
ncurses-libs-6.4-12.20240127.fc40.x86_64
ocaml-srpm-macros-10-1.fc41.noarch
openblas-srpm-macros-2-17.fc41.noarch
openldap-2.6.8-1.fc41.x86_64
openssl-libs-3.2.1-6.fc41.x86_64
p11-kit-0.25.3-4.fc40.x86_64
p11-kit-trust-0.25.3-4.fc40.x86_64
package-notes-srpm-macros-0.5-11.fc40.noarch
pam-1.6.1-3.fc41.x86_64
pam-libs-1.6.1-3.fc41.x86_64
patch-2.7.6-24.fc40.x86_64
pcre2-10.43-2.fc41.1.x86_64
pcre2-syntax-10.43-2.fc41.1.noarch
perl-srpm-macros-1-53.fc40.noarch
pkgconf-2.1.1-1.fc41.x86_64
pkgconf-m4-2.1.1-1.fc41.noarch
pkgconf-pkg-config-2.1.1-1.fc41.x86_64
popt-1.19-6.fc40.x86_64
publicsuffix-list-dafsa-20240107-3.fc40.noarch
pyproject-srpm-macros-1.12.0-1.fc40.noarch
python-srpm-macros-3.12-9.fc41.noarch
qt5-srpm-macros-5.15.13-1.fc41.noarch
qt6-srpm-macros-6.7.1-1.fc41.noarch
readline-8.2-8.fc40.x86_64
redhat-rpm-config-291-1.fc41.noarch
rpm-4.19.91-4.fc41.x86_64
rpm-build-4.19.91-4.fc41.x86_64
rpm-build-libs-4.19.91-4.fc41.x86_64
rpm-libs-4.19.91-4.fc41.x86_64
rpm-sequoia-1.6.0-3.fc41.x86_64
rust-srpm-macros-26.3-1.fc41.noarch
sed-4.9-1.fc40.x86_64
setup-2.15.0-3.fc41.noarch
shadow-utils-4.15.1-5.fc41.x86_64
sqlite-libs-3.45.3-1.fc41.x86_64
systemd-libs-256~rc3-3.fc41.x86_64
tar-1.35-3.fc40.x86_64
unzip-6.0-63.fc40.x86_64
util-linux-2.40.1-1.fc41.x86_64
util-linux-core-2.40.1-1.fc41.x86_64
which-2.21-41.fc40.x86_64
xxhash-libs-0.8.2-2.fc40.x86_64
xz-5.4.6-3.fc41.x86_64
xz-libs-5.4.6-3.fc41.x86_64
zig-srpm-macros-1-2.fc40.noarch
zip-3.0-40.fc40.x86_64
zlib-ng-compat-2.1.6-4.fc41.x86_64
zstd-1.5.6-1.fc41.x86_64
Start: buildsrpm
Start: rpmbuild -bs
Building target platforms: x86_64
Building for target x86_64
setting SOURCE_DATE_EPOCH=1706140800
Wrote: /builddir/build/SRPMS/mmseq-1.0.11-19.fc41.src.rpm
Finish: rpmbuild -bs
cp: preserving permissions for ‘/var/lib/copr-rpmbuild/results/chroot_scan/var/lib/mock/fedora-39-x86_64-1717081834.800473/root/var/log’: No such file or directory
INFO: chroot_scan: 3 files copied to /var/lib/copr-rpmbuild/results/chroot_scan
INFO: /var/lib/mock/fedora-39-x86_64-1717081834.800473/root/var/log/dnf.log
/var/lib/mock/fedora-39-x86_64-1717081834.800473/root/var/log/dnf.librepo.log
/var/lib/mock/fedora-39-x86_64-1717081834.800473/root/var/log/dnf.rpm.log
Finish: buildsrpm
INFO: Done(/var/lib/copr-rpmbuild/workspace/workdir-xx_bwfy8/mmseq/mmseq.spec) Config(child) 2 minutes 20 seconds
INFO: Results and/or logs in: /var/lib/copr-rpmbuild/results
INFO: Cleaning up build root ('cleanup_on_success=True')
Start: clean chroot
INFO: unmounting tmpfs.
Finish: clean chroot
INFO: Start(/var/lib/copr-rpmbuild/results/mmseq-1.0.11-19.fc41.src.rpm)  Config(fedora-39-x86_64)
Start(bootstrap): chroot init
INFO: mounting tmpfs at /var/lib/mock/fedora-39-x86_64-bootstrap-1717081834.800473/root.
INFO: reusing tmpfs at /var/lib/mock/fedora-39-x86_64-bootstrap-1717081834.800473/root.
INFO: calling preinit hooks
INFO: enabled root cache
INFO: enabled package manager cache
Start(bootstrap): cleaning package manager metadata
Finish(bootstrap): cleaning package manager metadata
Finish(bootstrap): chroot init
Start: chroot init
INFO: mounting tmpfs at /var/lib/mock/fedora-39-x86_64-1717081834.800473/root.
INFO: calling preinit hooks
INFO: enabled root cache
Start: unpacking root cache
Finish: unpacking root cache
INFO: enabled package manager cache
Start: cleaning package manager metadata
Finish: cleaning package manager metadata
INFO: enabled HW Info plugin
INFO: Buildroot is handled by package management downloaded with a bootstrap image:
  rpm-4.19.1.1-1.fc39.x86_64
  rpm-sequoia-1.6.0-1.fc39.x86_64
  python3-dnf-4.20.0-1.fc41.noarch
  python3-dnf-plugins-core-4.7.0-1.fc41.noarch
  dnf5-5.2.2.0-1.fc41.x86_64
Finish: chroot init
Start: build phase for mmseq-1.0.11-19.fc41.src.rpm
Start: build setup for mmseq-1.0.11-19.fc41.src.rpm
Building target platforms: x86_64
Building for target x86_64
setting SOURCE_DATE_EPOCH=1706140800
Wrote: /builddir/build/SRPMS/mmseq-1.0.11-19.fc41.src.rpm
No matches found for the following disable plugin patterns: local, spacewalk, versionlock
Copr repository                                  43 kB/s | 1.5 kB     00:00    
Additional repo http_kojipkgs_fedoraproject_org  48 kB/s | 3.8 kB     00:00    
fedora                                          917 kB/s |  25 kB     00:00    
updates                                         843 kB/s |  21 kB     00:00    
Dependencies resolved.
================================================================================================================================
 Package                       Arch    Version              Repository                                                      Size
================================================================================================================================
Installing:
 armadillo-devel               x86_64  12.8.1-1.fc41        http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch  2.0 M
 boost-devel                   x86_64  1.83.0-5.fc41        copr_base                                                       12 M
 flexiblas-devel               x86_64  3.4.4-1.fc41         copr_base                                                      113 k
 gcc-c++                       x86_64  14.1.1-4.fc41        http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   14 M
 gsl-devel                     x86_64  2.7.1-8.fc41         http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch  609 k
 htslib-devel                  x86_64  1.15.1-5.fc40        http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   99 k
 make                          x86_64  1:4.4.1-6.fc40       http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch  580 k
 perl-generators               noarch  1.16-5.fc40          http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   16 k
 zlib-ng-compat-devel          x86_64  2.1.6-4.fc41         http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   36 k
Installing dependencies:
 SuperLU                       x86_64  6.0.1-5.fc41         http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch  186 k
 SuperLU-devel                 x86_64  6.0.1-5.fc41         http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   27 k
 add-determinism               x86_64  0.2.0-9.fc41         http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch  907 k
 annobin-docs                  noarch  12.54-2.fc41         http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   90 k
 annobin-plugin-gcc            x86_64  12.54-2.fc41         http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch  965 k
 armadillo                     x86_64  12.8.1-1.fc41        http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   32 k
 arpack                        x86_64  3.9.1-3.fc40         copr_base                                                      211 k
 arpack-devel                  x86_64  3.9.1-3.fc40         copr_base                                                       22 k
 autoconf                      noarch  2.72-2.fc41          http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch  817 k
 automake                      noarch  1.16.5-16.fc40       http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch  676 k
 boost                         x86_64  1.83.0-5.fc41        copr_base                                                       14 k
 boost-atomic                  x86_64  1.83.0-5.fc41        copr_base                                                       20 k
 boost-chrono                  x86_64  1.83.0-5.fc41        copr_base                                                       26 k
 boost-container               x86_64  1.83.0-5.fc41        copr_base                                                       40 k
 boost-context                 x86_64  1.83.0-5.fc41        copr_base                                                       17 k
 boost-contract                x86_64  1.83.0-5.fc41        copr_base                                                       46 k
 boost-coroutine               x86_64  1.83.0-5.fc41        copr_base                                                       20 k
 boost-date-time               x86_64  1.83.0-5.fc41        copr_base                                                       15 k
 boost-fiber                   x86_64  1.83.0-5.fc41        copr_base                                                       42 k
 boost-filesystem              x86_64  1.83.0-5.fc41        copr_base                                                       69 k
 boost-graph                   x86_64  1.83.0-5.fc41        copr_base                                                      152 k
 boost-iostreams               x86_64  1.83.0-5.fc41        copr_base                                                       41 k
 boost-json                    x86_64  1.83.0-5.fc41        copr_base                                                      144 k
 boost-locale                  x86_64  1.83.0-5.fc41        copr_base                                                      213 k
 boost-log                     x86_64  1.83.0-5.fc41        copr_base                                                      490 k
 boost-math                    x86_64  1.83.0-5.fc41        copr_base                                                      215 k
 boost-nowide                  x86_64  1.83.0-5.fc41        copr_base                                                       20 k
 boost-numpy3                  x86_64  1.83.0-5.fc41        copr_base                                                       29 k
 boost-program-options         x86_64  1.83.0-5.fc41        copr_base                                                      109 k
 boost-python3                 x86_64  1.83.0-5.fc41        copr_base                                                       96 k
 boost-random                  x86_64  1.83.0-5.fc41        copr_base                                                       24 k
 boost-regex                   x86_64  1.83.0-5.fc41        copr_base                                                      111 k
 boost-serialization           x86_64  1.83.0-5.fc41        copr_base                                                      134 k
 boost-stacktrace              x86_64  1.83.0-5.fc41        copr_base                                                       30 k
 boost-system                  x86_64  1.83.0-5.fc41        copr_base                                                       15 k
 boost-test                    x86_64  1.83.0-5.fc41        copr_base                                                      238 k
 boost-thread                  x86_64  1.83.0-5.fc41        copr_base                                                       62 k
 boost-timer                   x86_64  1.83.0-5.fc41        copr_base                                                       21 k
 boost-type_erasure            x86_64  1.83.0-5.fc41        copr_base                                                       34 k
 boost-wave                    x86_64  1.83.0-5.fc41        copr_base                                                      207 k
 cmake-filesystem              x86_64  3.28.3-4.fc41        http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   18 k
 cpp                           x86_64  14.1.1-4.fc41        http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   12 M
 emacs-filesystem              noarch  1:30.0-2.fc41        http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch  7.1 k
 expat                         x86_64  2.6.2-1.fc41         http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch  113 k
 flexiblas                     x86_64  3.4.4-1.fc41         copr_base                                                       26 k
 flexiblas-netlib              x86_64  3.4.4-1.fc41         copr_base                                                      3.2 M
 flexiblas-netlib64            x86_64  3.4.4-1.fc41         copr_base                                                      3.0 M
 flexiblas-openblas-openmp     x86_64  3.4.4-1.fc41         copr_base                                                       18 k
 flexiblas-openblas-openmp64   x86_64  3.4.4-1.fc41         copr_base                                                       18 k
 gc                            x86_64  8.2.2-6.fc40         http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch  110 k
 gcc                           x86_64  14.1.1-4.fc41        http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   37 M
 gcc-gfortran                  x86_64  14.1.1-4.fc41        http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   13 M
 gcc-plugin-annobin            x86_64  14.1.1-4.fc41        http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   51 k
 glibc-devel                   x86_64  2.39.9000-18.fc41    http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch  122 k
 glibc-headers-x86             noarch  2.39.9000-18.fc41    http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch  542 k
 groff-base                    x86_64  1.23.0-6.fc40        http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch  1.1 M
 gsl                           x86_64  2.7.1-8.fc41         http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch  1.1 M
 guile30                       x86_64  3.0.9-1.fc41         http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch  8.2 M
 hdf5                          x86_64  1.12.1-15.fc40       http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch  2.2 M
 hdf5-devel                    x86_64  1.12.1-15.fc40       http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch  1.3 M
 htslib                        x86_64  1.15.1-5.fc40        http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch  493 k
 kernel-headers                x86_64  6.10.0-0.rc1.17.fc41 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch  1.5 M
 libaec                        x86_64  1.1.2-1.fc40         http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   37 k
 libaec-devel                  x86_64  1.1.2-1.fc40         http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   12 k
 libb2                         x86_64  0.98.1-11.fc40       http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   25 k
 libgfortran                   x86_64  14.1.1-4.fc41        http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch  934 k
 libicu                        x86_64  74.2-1.fc40          http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   10 M
 libicu-devel                  x86_64  74.2-1.fc40          http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch  855 k
 libmpc                        x86_64  1.3.1-5.fc40         http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   71 k
 libquadmath                   x86_64  14.1.1-4.fc41        http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch  198 k
 libquadmath-devel             x86_64  14.1.1-4.fc41        http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   40 k
 libstdc++-devel               x86_64  14.1.1-4.fc41        http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch  2.6 M
 libxcrypt-devel               x86_64  4.4.36-5.fc40        http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   29 k
 m4                            x86_64  1.4.19-9.fc40        http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch  298 k
 metis                         x86_64  5.1.0.3-5.fc40       http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch  571 k
 mpdecimal                     x86_64  2.5.1-9.fc40         http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   89 k
 ncurses                       x86_64  6.4-12.20240127.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch  416 k
 openblas                      x86_64  0.3.26-4.fc40        http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   39 k
 openblas-openmp               x86_64  0.3.26-4.fc40        http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch  5.1 M
 openblas-openmp64             x86_64  0.3.26-4.fc40        http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch  4.9 M
 perl-AutoLoader               noarch  5.74-507.fc41        http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   21 k
 perl-B                        x86_64  1.88-507.fc41        http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch  176 k
 perl-Carp                     noarch  1.54-502.fc40        http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   29 k
 perl-Class-Struct             noarch  0.68-507.fc41        http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   22 k
 perl-Data-Dumper              x86_64  2.188-503.fc40       http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   56 k
 perl-Digest                   noarch  1.20-502.fc40        http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   25 k
 perl-Digest-MD5               x86_64  2.59-3.fc40          http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   36 k
 perl-DynaLoader               x86_64  1.54-507.fc41        http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   26 k
 perl-Encode                   x86_64  4:3.21-505.fc41      http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch  1.0 M
 perl-Errno                    x86_64  1.37-507.fc41        http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   15 k
 perl-Exporter                 noarch  5.78-3.fc40          http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   31 k
 perl-Fcntl                    x86_64  1.15-507.fc41        http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   20 k
 perl-Fedora-VSP               noarch  0.001-34.fc40        http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   23 k
 perl-File-Basename            noarch  2.86-507.fc41        http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   17 k
 perl-File-Compare             noarch  1.100.700-507.fc41   http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   13 k
 perl-File-Copy                noarch  2.41-507.fc41        http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   20 k
 perl-File-Find                noarch  1.43-507.fc41        http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   25 k
 perl-File-Path                noarch  2.18-503.fc40        http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   35 k
 perl-File-Temp                noarch  1:0.231.100-503.fc40 http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   59 k
 perl-File-stat                noarch  1.13-507.fc41        http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   17 k
 perl-FileHandle               noarch  2.05-507.fc41        http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   16 k
 perl-Getopt-Long              noarch  1:2.57-4.fc41        http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   63 k
 perl-Getopt-Std               noarch  1.13-507.fc41        http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   16 k
 perl-HTTP-Tiny                noarch  0.088-5.fc40         http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   56 k
 perl-IO                       x86_64  1.52-507.fc41        http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   78 k
 perl-IO-Socket-IP             noarch  0.42-2.fc40          http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   42 k
 perl-IO-Socket-SSL            noarch  2.085-1.fc40         http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch  225 k
 perl-IPC-Open3                noarch  1.22-507.fc41        http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   22 k
 perl-MIME-Base64              x86_64  3.16-503.fc40        http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   30 k
 perl-Mozilla-CA               noarch  20240313-1.fc41      http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   14 k
 perl-Net-SSLeay               x86_64  1.94-3.fc40          http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch  366 k
 perl-POSIX                    x86_64  2.13-507.fc41        http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   96 k
 perl-PathTools                x86_64  3.89-502.fc40        http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   83 k
 perl-Pod-Escapes              noarch  1:1.07-503.fc40      http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   20 k
 perl-Pod-Perldoc              noarch  3.28.01-503.fc40     http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   79 k
 perl-Pod-Simple               noarch  1:3.45-6.fc40        http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch  209 k
 perl-Pod-Usage                noarch  4:2.03-504.fc41      http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   40 k
 perl-Scalar-List-Utils        x86_64  5:1.63-503.fc40      http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   73 k
 perl-SelectSaver              noarch  1.02-507.fc41        http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   12 k
 perl-Socket                   x86_64  4:2.038-1.fc41       http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   55 k
 perl-Storable                 x86_64  1:3.32-502.fc40      http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   98 k
 perl-Symbol                   noarch  1.09-507.fc41        http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   14 k
 perl-Term-ANSIColor           noarch  5.01-504.fc40        http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   48 k
 perl-Term-Cap                 noarch  1.18-503.fc40        http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   22 k
 perl-Text-ParseWords          noarch  3.31-502.fc40        http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   16 k
 perl-Text-Tabs+Wrap           noarch  2024.001-1.fc41      http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   22 k
 perl-Thread-Queue             noarch  3.14-503.fc40        http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   21 k
 perl-Time-Local               noarch  2:1.350-5.fc40       http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   34 k
 perl-URI                      noarch  5.28-1.fc41          http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch  120 k
 perl-base                     noarch  2.27-507.fc41        http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   16 k
 perl-constant                 noarch  1.33-503.fc40        http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   23 k
 perl-if                       noarch  0.61.000-507.fc41    http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   14 k
 perl-interpreter              x86_64  4:5.38.2-507.fc41    http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   72 k
 perl-libnet                   noarch  3.15-503.fc40        http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch  122 k
 perl-libs                     x86_64  4:5.38.2-507.fc41    http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch  2.2 M
 perl-locale                   noarch  1.10-507.fc41        http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   14 k
 perl-macros                   noarch  4:5.38.2-507.fc41    http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   12 k
 perl-mro                      x86_64  1.28-507.fc41        http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   29 k
 perl-overload                 noarch  1.37-507.fc41        http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   46 k
 perl-overloading              noarch  0.02-507.fc41        http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   13 k
 perl-parent                   noarch  1:0.241-502.fc40     http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   15 k
 perl-podlators                noarch  1:5.01-502.fc40      http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch  121 k
 perl-threads                  x86_64  1:2.36-503.fc40      http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   58 k
 perl-threads-shared           x86_64  1.68-502.fc40        http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   45 k
 perl-vars                     noarch  1.05-507.fc41        http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   13 k
 python-pip-wheel              noarch  24.0-2.fc41          http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch  1.5 M
 python3                       x86_64  3.12.3-2.fc41        http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch   27 k
 python3-libs                  x86_64  3.12.3-2.fc41        http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch  8.8 M
 python3-numpy                 x86_64  1:1.26.4-4.fc41      copr_base                                                      7.2 M
 tzdata                        noarch  2024a-8.fc41         http_kojipkgs_fedoraproject_org_repos_rawhide_latest_basearch  431 k

Transaction Summary
================================================================================================================================
Install  159 Packages

Total download size: 172 M
Installed size: 742 M
Downloading Packages:
(1/159): boost-1.83.0-5.fc41.x86_64.rpm         323 kB/s |  14 kB     00:00    
(2/159): arpack-devel-3.9.1-3.fc40.x86_64.rpm   433 kB/s |  22 kB     00:00    
(3/159): boost-atomic-1.83.0-5.fc41.x86_64.rpm  2.0 MB/s |  20 kB     00:00    
(4/159): boost-chrono-1.83.0-5.fc41.x86_64.rpm  2.3 MB/s |  26 kB     00:00    
(5/159): boost-container-1.83.0-5.fc41.x86_64.r 2.1 MB/s |  40 kB     00:00    
(6/159): arpack-3.9.1-3.fc40.x86_64.rpm         2.3 MB/s | 211 kB     00:00    
(7/159): boost-context-1.83.0-5.fc41.x86_64.rpm 660 kB/s |  17 kB     00:00    
(8/159): boost-contract-1.83.0-5.fc41.x86_64.rp 2.5 MB/s |  46 kB     00:00    
(9/159): boost-coroutine-1.83.0-5.fc41.x86_64.r 1.8 MB/s |  20 kB     00:00    
(10/159): boost-date-time-1.83.0-5.fc41.x86_64. 1.4 MB/s |  15 kB     00:00    
(11/159): boost-fiber-1.83.0-5.fc41.x86_64.rpm  1.3 MB/s |  42 kB     00:00    
(12/159): boost-filesystem-1.83.0-5.fc41.x86_64 2.1 MB/s |  69 kB     00:00    
(13/159): boost-graph-1.83.0-5.fc41.x86_64.rpm  1.7 MB/s | 152 kB     00:00    
(14/159): boost-iostreams-1.83.0-5.fc41.x86_64. 480 kB/s |  41 kB     00:00    
(15/159): boost-devel-1.83.0-5.fc41.x86_64.rpm   78 MB/s |  12 MB     00:00    
(16/159): boost-json-1.83.0-5.fc41.x86_64.rpm   6.5 MB/s | 144 kB     00:00    
(17/159): boost-locale-1.83.0-5.fc41.x86_64.rpm 9.5 MB/s | 213 kB     00:00    
(18/159): boost-log-1.83.0-5.fc41.x86_64.rpm     31 MB/s | 490 kB     00:00    
(19/159): boost-math-1.83.0-5.fc41.x86_64.rpm    13 MB/s | 215 kB     00:00    
(20/159): boost-nowide-1.83.0-5.fc41.x86_64.rpm 1.2 MB/s |  20 kB     00:00    
(21/159): boost-numpy3-1.83.0-5.fc41.x86_64.rpm 3.0 MB/s |  29 kB     00:00    
(22/159): boost-program-options-1.83.0-5.fc41.x  10 MB/s | 109 kB     00:00    
(23/159): boost-python3-1.83.0-5.fc41.x86_64.rp 8.4 MB/s |  96 kB     00:00    
(24/159): boost-random-1.83.0-5.fc41.x86_64.rpm 2.6 MB/s |  24 kB     00:00    
(25/159): boost-regex-1.83.0-5.fc41.x86_64.rpm  9.2 MB/s | 111 kB     00:00    
(26/159): boost-serialization-1.83.0-5.fc41.x86  11 MB/s | 134 kB     00:00    
(27/159): boost-stacktrace-1.83.0-5.fc41.x86_64 3.2 MB/s |  30 kB     00:00    
(28/159): boost-system-1.83.0-5.fc41.x86_64.rpm 1.7 MB/s |  15 kB     00:00    
(29/159): boost-test-1.83.0-5.fc41.x86_64.rpm    19 MB/s | 238 kB     00:00    
(30/159): boost-thread-1.83.0-5.fc41.x86_64.rpm 6.0 MB/s |  62 kB     00:00    
(31/159): boost-timer-1.83.0-5.fc41.x86_64.rpm  2.2 MB/s |  21 kB     00:00    
(32/159): boost-type_erasure-1.83.0-5.fc41.x86_ 3.2 MB/s |  34 kB     00:00    
(33/159): boost-wave-1.83.0-5.fc41.x86_64.rpm    15 MB/s | 207 kB     00:00    
(34/159): flexiblas-3.4.4-1.fc41.x86_64.rpm     2.6 MB/s |  26 kB     00:00    
(35/159): flexiblas-devel-3.4.4-1.fc41.x86_64.r  10 MB/s | 113 kB     00:00    
(36/159): flexiblas-openblas-openmp-3.4.4-1.fc4 534 kB/s |  18 kB     00:00    
(37/159): flexiblas-netlib64-3.4.4-1.fc41.x86_6  67 MB/s | 3.0 MB     00:00    
(38/159): flexiblas-openblas-openmp64-3.4.4-1.f 781 kB/s |  18 kB     00:00    
(39/159): flexiblas-netlib-3.4.4-1.fc41.x86_64.  30 MB/s | 3.2 MB     00:00    
(40/159): python3-numpy-1.26.4-4.fc41.x86_64.rp  75 MB/s | 7.2 MB     00:00    
(41/159): SuperLU-devel-6.0.1-5.fc41.x86_64.rpm 444 kB/s |  27 kB     00:00    
(42/159): SuperLU-6.0.1-5.fc41.x86_64.rpm       1.7 MB/s | 186 kB     00:00    
(43/159): annobin-docs-12.54-2.fc41.noarch.rpm  4.4 MB/s |  90 kB     00:00    
(44/159): armadillo-12.8.1-1.fc41.x86_64.rpm    1.4 MB/s |  32 kB     00:00    
(45/159): annobin-plugin-gcc-12.54-2.fc41.x86_6  16 MB/s | 965 kB     00:00    
(46/159): add-determinism-0.2.0-9.fc41.x86_64.r 8.2 MB/s | 907 kB     00:00    
(47/159): autoconf-2.72-2.fc41.noarch.rpm        29 MB/s | 817 kB     00:00    
(48/159): automake-1.16.5-16.fc40.noarch.rpm     24 MB/s | 676 kB     00:00    
(49/159): cmake-filesystem-3.28.3-4.fc41.x86_64 676 kB/s |  18 kB     00:00    
(50/159): emacs-filesystem-30.0-2.fc41.noarch.r 273 kB/s | 7.1 kB     00:00    
(51/159): armadillo-devel-12.8.1-1.fc41.x86_64.  19 MB/s | 2.0 MB     00:00    
(52/159): expat-2.6.2-1.fc41.x86_64.rpm         3.3 MB/s | 113 kB     00:00    
(53/159): gc-8.2.2-6.fc40.x86_64.rpm            2.8 MB/s | 110 kB     00:00    
(54/159): cpp-14.1.1-4.fc41.x86_64.rpm           57 MB/s |  12 MB     00:00    
(55/159): gcc-gfortran-14.1.1-4.fc41.x86_64.rpm  34 MB/s |  13 MB     00:00    
(56/159): gcc-c++-14.1.1-4.fc41.x86_64.rpm       26 MB/s |  14 MB     00:00    
(57/159): gcc-plugin-annobin-14.1.1-4.fc41.x86_ 1.4 MB/s |  51 kB     00:00    
(58/159): glibc-devel-2.39.9000-18.fc41.x86_64. 4.6 MB/s | 122 kB     00:00    
(59/159): glibc-headers-x86-2.39.9000-18.fc41.n  16 MB/s | 542 kB     00:00    
(60/159): groff-base-1.23.0-6.fc40.x86_64.rpm    23 MB/s | 1.1 MB     00:00    
(61/159): gsl-2.7.1-8.fc41.x86_64.rpm            28 MB/s | 1.1 MB     00:00    
(62/159): gsl-devel-2.7.1-8.fc41.x86_64.rpm      18 MB/s | 609 kB     00:00    
(63/159): hdf5-1.12.1-15.fc40.x86_64.rpm         19 MB/s | 2.2 MB     00:00    
(64/159): guile30-3.0.9-1.fc41.x86_64.rpm        46 MB/s | 8.2 MB     00:00    
(65/159): hdf5-devel-1.12.1-15.fc40.x86_64.rpm   20 MB/s | 1.3 MB     00:00    
(66/159): gcc-14.1.1-4.fc41.x86_64.rpm           40 MB/s |  37 MB     00:00    
(67/159): htslib-1.15.1-5.fc40.x86_64.rpm       5.4 MB/s | 493 kB     00:00    
(68/159): htslib-devel-1.15.1-5.fc40.x86_64.rpm 1.4 MB/s |  99 kB     00:00    
(69/159): libaec-1.1.2-1.fc40.x86_64.rpm        1.4 MB/s |  37 kB     00:00    
(70/159): kernel-headers-6.10.0-0.rc1.17.fc41.x  40 MB/s | 1.5 MB     00:00    
(71/159): libaec-devel-1.1.2-1.fc40.x86_64.rpm  327 kB/s |  12 kB     00:00    
(72/159): libb2-0.98.1-11.fc40.x86_64.rpm       1.2 MB/s |  25 kB     00:00    
(73/159): libgfortran-14.1.1-4.fc41.x86_64.rpm   19 MB/s | 934 kB     00:00    
(74/159): libicu-devel-74.2-1.fc40.x86_64.rpm    17 MB/s | 855 kB     00:00    
(75/159): libmpc-1.3.1-5.fc40.x86_64.rpm        2.8 MB/s |  71 kB     00:00    
(76/159): libquadmath-14.1.1-4.fc41.x86_64.rpm  6.8 MB/s | 198 kB     00:00    
(77/159): libquadmath-devel-14.1.1-4.fc41.x86_6 1.5 MB/s |  40 kB     00:00    
(78/159): libxcrypt-devel-4.4.36-5.fc40.x86_64. 882 kB/s |  29 kB     00:00    
(79/159): libstdc++-devel-14.1.1-4.fc41.x86_64.  33 MB/s | 2.6 MB     00:00    
(80/159): m4-1.4.19-9.fc40.x86_64.rpm           7.9 MB/s | 298 kB     00:00    
(81/159): libicu-74.2-1.fc40.x86_64.rpm          54 MB/s |  10 MB     00:00    
(82/159): make-4.4.1-6.fc40.x86_64.rpm           21 MB/s | 580 kB     00:00    
(83/159): metis-5.1.0.3-5.fc40.x86_64.rpm        15 MB/s | 571 kB     00:00    
(84/159): mpdecimal-2.5.1-9.fc40.x86_64.rpm     3.7 MB/s |  89 kB     00:00    
(85/159): ncurses-6.4-12.20240127.fc40.x86_64.r  17 MB/s | 416 kB     00:00    
(86/159): openblas-0.3.26-4.fc40.x86_64.rpm     1.9 MB/s |  39 kB     00:00    
(87/159): perl-AutoLoader-5.74-507.fc41.noarch. 548 kB/s |  21 kB     00:00    
(88/159): perl-B-1.88-507.fc41.x86_64.rpm       5.0 MB/s | 176 kB     00:00    
(89/159): perl-Carp-1.54-502.fc40.noarch.rpm    939 kB/s |  29 kB     00:00    
(90/159): openblas-openmp64-0.3.26-4.fc40.x86_6  38 MB/s | 4.9 MB     00:00    
(91/159): openblas-openmp-0.3.26-4.fc40.x86_64.  36 MB/s | 5.1 MB     00:00    
(92/159): perl-Class-Struct-0.68-507.fc41.noarc 1.0 MB/s |  22 kB     00:00    
(93/159): perl-Data-Dumper-2.188-503.fc40.x86_6 2.8 MB/s |  56 kB     00:00    
(94/159): perl-Digest-1.20-502.fc40.noarch.rpm  1.3 MB/s |  25 kB     00:00    
(95/159): perl-Digest-MD5-2.59-3.fc40.x86_64.rp 1.9 MB/s |  36 kB     00:00    
(96/159): perl-DynaLoader-1.54-507.fc41.x86_64. 1.3 MB/s |  26 kB     00:00    
(97/159): perl-Errno-1.37-507.fc41.x86_64.rpm   680 kB/s |  15 kB     00:00    
(98/159): perl-Exporter-5.78-3.fc40.noarch.rpm  1.5 MB/s |  31 kB     00:00    
(99/159): perl-Encode-3.21-505.fc41.x86_64.rpm   27 MB/s | 1.0 MB     00:00    
(100/159): perl-Fcntl-1.15-507.fc41.x86_64.rpm  933 kB/s |  20 kB     00:00    
(101/159): perl-File-Basename-2.86-507.fc41.noa 902 kB/s |  17 kB     00:00    
(102/159): perl-Fedora-VSP-0.001-34.fc40.noarch 1.1 MB/s |  23 kB     00:00    
(103/159): perl-File-Compare-1.100.700-507.fc41 630 kB/s |  13 kB     00:00    
(104/159): perl-File-Copy-2.41-507.fc41.noarch. 1.0 MB/s |  20 kB     00:00    
(105/159): perl-File-Find-1.43-507.fc41.noarch. 1.2 MB/s |  25 kB     00:00    
(106/159): perl-File-Path-2.18-503.fc40.noarch. 1.8 MB/s |  35 kB     00:00    
(107/159): perl-File-Temp-0.231.100-503.fc40.no 2.8 MB/s |  59 kB     00:00    
(108/159): perl-File-stat-1.13-507.fc41.noarch. 898 kB/s |  17 kB     00:00    
(109/159): perl-FileHandle-2.05-507.fc41.noarch 788 kB/s |  16 kB     00:00    
(110/159): perl-Getopt-Std-1.13-507.fc41.noarch 684 kB/s |  16 kB     00:00    
(111/159): perl-Getopt-Long-2.57-4.fc41.noarch. 2.5 MB/s |  63 kB     00:00    
(112/159): perl-HTTP-Tiny-0.088-5.fc40.noarch.r 2.8 MB/s |  56 kB     00:00    
(113/159): perl-IO-Socket-IP-0.42-2.fc40.noarch 2.2 MB/s |  42 kB     00:00    
(114/159): perl-IO-Socket-SSL-2.085-1.fc40.noar  10 MB/s | 225 kB     00:00    
(115/159): perl-IO-1.52-507.fc41.x86_64.rpm     3.0 MB/s |  78 kB     00:00    
(116/159): perl-IPC-Open3-1.22-507.fc41.noarch. 1.0 MB/s |  22 kB     00:00    
(117/159): perl-MIME-Base64-3.16-503.fc40.x86_6 1.2 MB/s |  30 kB     00:00    
(118/159): perl-Mozilla-CA-20240313-1.fc41.noar 592 kB/s |  14 kB     00:00    
(119/159): perl-Net-SSLeay-1.94-3.fc40.x86_64.r  15 MB/s | 366 kB     00:00    
(120/159): perl-PathTools-3.89-502.fc40.x86_64. 3.8 MB/s |  83 kB     00:00    
(121/159): perl-POSIX-2.13-507.fc41.x86_64.rpm  4.2 MB/s |  96 kB     00:00    
(122/159): perl-Pod-Escapes-1.07-503.fc40.noarc 1.0 MB/s |  20 kB     00:00    
(123/159): perl-Pod-Perldoc-3.28.01-503.fc40.no 4.0 MB/s |  79 kB     00:00    
(124/159): perl-Pod-Simple-3.45-6.fc40.noarch.r 9.9 MB/s | 209 kB     00:00    
(125/159): perl-Pod-Usage-2.03-504.fc41.noarch. 2.0 MB/s |  40 kB     00:00    
(126/159): perl-Scalar-List-Utils-1.63-503.fc40 3.4 MB/s |  73 kB     00:00    
(127/159): perl-SelectSaver-1.02-507.fc41.noarc 609 kB/s |  12 kB     00:00    
(128/159): perl-Socket-2.038-1.fc41.x86_64.rpm  2.3 MB/s |  55 kB     00:00    
(129/159): perl-Symbol-1.09-507.fc41.noarch.rpm 748 kB/s |  14 kB     00:00    
(130/159): perl-Storable-3.32-502.fc40.x86_64.r 4.7 MB/s |  98 kB     00:00    
(131/159): perl-Term-ANSIColor-5.01-504.fc40.no 2.5 MB/s |  48 kB     00:00    
(132/159): perl-Term-Cap-1.18-503.fc40.noarch.r 1.1 MB/s |  22 kB     00:00    
(133/159): perl-Text-ParseWords-3.31-502.fc40.n 867 kB/s |  16 kB     00:00    
(134/159): perl-Text-Tabs+Wrap-2024.001-1.fc41. 1.1 MB/s |  22 kB     00:00    
(135/159): perl-Thread-Queue-3.14-503.fc40.noar 1.0 MB/s |  21 kB     00:00    
(136/159): perl-Time-Local-1.350-5.fc40.noarch. 1.7 MB/s |  34 kB     00:00    
(137/159): perl-URI-5.28-1.fc41.noarch.rpm      6.0 MB/s | 120 kB     00:00    
(138/159): perl-base-2.27-507.fc41.noarch.rpm   875 kB/s |  16 kB     00:00    
(139/159): perl-constant-1.33-503.fc40.noarch.r 1.1 MB/s |  23 kB     00:00    
(140/159): perl-generators-1.16-5.fc40.noarch.r 800 kB/s |  16 kB     00:00    
(141/159): perl-if-0.61.000-507.fc41.noarch.rpm 688 kB/s |  14 kB     00:00    
(142/159): perl-interpreter-5.38.2-507.fc41.x86 3.1 MB/s |  72 kB     00:00    
(143/159): perl-libnet-3.15-503.fc40.noarch.rpm 6.3 MB/s | 122 kB     00:00    
(144/159): perl-locale-1.10-507.fc41.noarch.rpm 618 kB/s |  14 kB     00:00    
(145/159): perl-macros-5.38.2-507.fc41.noarch.r 595 kB/s |  12 kB     00:00    
(146/159): perl-libs-5.38.2-507.fc41.x86_64.rpm  48 MB/s | 2.2 MB     00:00    
(147/159): perl-mro-1.28-507.fc41.x86_64.rpm    1.3 MB/s |  29 kB     00:00    
(148/159): perl-overload-1.37-507.fc41.noarch.r 2.4 MB/s |  46 kB     00:00    
(149/159): perl-overloading-0.02-507.fc41.noarc 698 kB/s |  13 kB     00:00    
(150/159): perl-parent-0.241-502.fc40.noarch.rp 799 kB/s |  15 kB     00:00    
(151/159): perl-podlators-5.01-502.fc40.noarch. 5.2 MB/s | 121 kB     00:00    
(152/159): perl-threads-shared-1.68-502.fc40.x8 1.9 MB/s |  45 kB     00:00    
(153/159): perl-threads-2.36-503.fc40.x86_64.rp 2.2 MB/s |  58 kB     00:00    
(154/159): perl-vars-1.05-507.fc41.noarch.rpm   695 kB/s |  13 kB     00:00    
(155/159): python3-3.12.3-2.fc41.x86_64.rpm     1.2 MB/s |  27 kB     00:00    
(156/159): python-pip-wheel-24.0-2.fc41.noarch.  33 MB/s | 1.5 MB     00:00    
(157/159): tzdata-2024a-8.fc41.noarch.rpm        15 MB/s | 431 kB     00:00    
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(159/159): python3-libs-3.12.3-2.fc41.x86_64.rp  63 MB/s | 8.8 MB     00:00    
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Total                                            67 MB/s | 172 MB     00:02     
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Installed:
  SuperLU-6.0.1-5.fc41.x86_64                                                   
  SuperLU-devel-6.0.1-5.fc41.x86_64                                             
  add-determinism-0.2.0-9.fc41.x86_64                                           
  annobin-docs-12.54-2.fc41.noarch                                              
  annobin-plugin-gcc-12.54-2.fc41.x86_64                                        
  armadillo-12.8.1-1.fc41.x86_64                                                
  armadillo-devel-12.8.1-1.fc41.x86_64                                          
  arpack-3.9.1-3.fc40.x86_64                                                    
  arpack-devel-3.9.1-3.fc40.x86_64                                              
  autoconf-2.72-2.fc41.noarch                                                   
  automake-1.16.5-16.fc40.noarch                                                
  boost-1.83.0-5.fc41.x86_64                                                    
  boost-atomic-1.83.0-5.fc41.x86_64                                             
  boost-chrono-1.83.0-5.fc41.x86_64                                             
  boost-container-1.83.0-5.fc41.x86_64                                          
  boost-context-1.83.0-5.fc41.x86_64                                            
  boost-contract-1.83.0-5.fc41.x86_64                                           
  boost-coroutine-1.83.0-5.fc41.x86_64                                          
  boost-date-time-1.83.0-5.fc41.x86_64                                          
  boost-devel-1.83.0-5.fc41.x86_64                                              
  boost-fiber-1.83.0-5.fc41.x86_64                                              
  boost-filesystem-1.83.0-5.fc41.x86_64                                         
  boost-graph-1.83.0-5.fc41.x86_64                                              
  boost-iostreams-1.83.0-5.fc41.x86_64                                          
  boost-json-1.83.0-5.fc41.x86_64                                               
  boost-locale-1.83.0-5.fc41.x86_64                                             
  boost-log-1.83.0-5.fc41.x86_64                                                
  boost-math-1.83.0-5.fc41.x86_64                                               
  boost-nowide-1.83.0-5.fc41.x86_64                                             
  boost-numpy3-1.83.0-5.fc41.x86_64                                             
  boost-program-options-1.83.0-5.fc41.x86_64                                    
  boost-python3-1.83.0-5.fc41.x86_64                                            
  boost-random-1.83.0-5.fc41.x86_64                                             
  boost-regex-1.83.0-5.fc41.x86_64                                              
  boost-serialization-1.83.0-5.fc41.x86_64                                      
  boost-stacktrace-1.83.0-5.fc41.x86_64                                         
  boost-system-1.83.0-5.fc41.x86_64                                             
  boost-test-1.83.0-5.fc41.x86_64                                               
  boost-thread-1.83.0-5.fc41.x86_64                                             
  boost-timer-1.83.0-5.fc41.x86_64                                              
  boost-type_erasure-1.83.0-5.fc41.x86_64                                       
  boost-wave-1.83.0-5.fc41.x86_64                                               
  cmake-filesystem-3.28.3-4.fc41.x86_64                                         
  cpp-14.1.1-4.fc41.x86_64                                                      
  emacs-filesystem-1:30.0-2.fc41.noarch                                         
  expat-2.6.2-1.fc41.x86_64                                                     
  flexiblas-3.4.4-1.fc41.x86_64                                                 
  flexiblas-devel-3.4.4-1.fc41.x86_64                                           
  flexiblas-netlib-3.4.4-1.fc41.x86_64                                          
  flexiblas-netlib64-3.4.4-1.fc41.x86_64                                        
  flexiblas-openblas-openmp-3.4.4-1.fc41.x86_64                                 
  flexiblas-openblas-openmp64-3.4.4-1.fc41.x86_64                               
  gc-8.2.2-6.fc40.x86_64                                                        
  gcc-14.1.1-4.fc41.x86_64                                                      
  gcc-c++-14.1.1-4.fc41.x86_64                                                  
  gcc-gfortran-14.1.1-4.fc41.x86_64                                             
  gcc-plugin-annobin-14.1.1-4.fc41.x86_64                                       
  glibc-devel-2.39.9000-18.fc41.x86_64                                          
  glibc-headers-x86-2.39.9000-18.fc41.noarch                                    
  groff-base-1.23.0-6.fc40.x86_64                                               
  gsl-2.7.1-8.fc41.x86_64                                                       
  gsl-devel-2.7.1-8.fc41.x86_64                                                 
  guile30-3.0.9-1.fc41.x86_64                                                   
  hdf5-1.12.1-15.fc40.x86_64                                                    
  hdf5-devel-1.12.1-15.fc40.x86_64                                              
  htslib-1.15.1-5.fc40.x86_64                                                   
  htslib-devel-1.15.1-5.fc40.x86_64                                             
  kernel-headers-6.10.0-0.rc1.17.fc41.x86_64                                    
  libaec-1.1.2-1.fc40.x86_64                                                    
  libaec-devel-1.1.2-1.fc40.x86_64                                              
  libb2-0.98.1-11.fc40.x86_64                                                   
  libgfortran-14.1.1-4.fc41.x86_64                                              
  libicu-74.2-1.fc40.x86_64                                                     
  libicu-devel-74.2-1.fc40.x86_64                                               
  libmpc-1.3.1-5.fc40.x86_64                                                    
  libquadmath-14.1.1-4.fc41.x86_64                                              
  libquadmath-devel-14.1.1-4.fc41.x86_64                                        
  libstdc++-devel-14.1.1-4.fc41.x86_64                                          
  libxcrypt-devel-4.4.36-5.fc40.x86_64                                          
  m4-1.4.19-9.fc40.x86_64                                                       
  make-1:4.4.1-6.fc40.x86_64                                                    
  metis-5.1.0.3-5.fc40.x86_64                                                   
  mpdecimal-2.5.1-9.fc40.x86_64                                                 
  ncurses-6.4-12.20240127.fc40.x86_64                                           
  openblas-0.3.26-4.fc40.x86_64                                                 
  openblas-openmp-0.3.26-4.fc40.x86_64                                          
  openblas-openmp64-0.3.26-4.fc40.x86_64                                        
  perl-AutoLoader-5.74-507.fc41.noarch                                          
  perl-B-1.88-507.fc41.x86_64                                                   
  perl-Carp-1.54-502.fc40.noarch                                                
  perl-Class-Struct-0.68-507.fc41.noarch                                        
  perl-Data-Dumper-2.188-503.fc40.x86_64                                        
  perl-Digest-1.20-502.fc40.noarch                                              
  perl-Digest-MD5-2.59-3.fc40.x86_64                                            
  perl-DynaLoader-1.54-507.fc41.x86_64                                          
  perl-Encode-4:3.21-505.fc41.x86_64                                            
  perl-Errno-1.37-507.fc41.x86_64                                               
  perl-Exporter-5.78-3.fc40.noarch                                              
  perl-Fcntl-1.15-507.fc41.x86_64                                               
  perl-Fedora-VSP-0.001-34.fc40.noarch                                          
  perl-File-Basename-2.86-507.fc41.noarch                                       
  perl-File-Compare-1.100.700-507.fc41.noarch                                   
  perl-File-Copy-2.41-507.fc41.noarch                                           
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  perl-File-Path-2.18-503.fc40.noarch                                           
  perl-File-Temp-1:0.231.100-503.fc40.noarch                                    
  perl-File-stat-1.13-507.fc41.noarch                                           
  perl-FileHandle-2.05-507.fc41.noarch                                          
  perl-Getopt-Long-1:2.57-4.fc41.noarch                                         
  perl-Getopt-Std-1.13-507.fc41.noarch                                          
  perl-HTTP-Tiny-0.088-5.fc40.noarch                                            
  perl-IO-1.52-507.fc41.x86_64                                                  
  perl-IO-Socket-IP-0.42-2.fc40.noarch                                          
  perl-IO-Socket-SSL-2.085-1.fc40.noarch                                        
  perl-IPC-Open3-1.22-507.fc41.noarch                                           
  perl-MIME-Base64-3.16-503.fc40.x86_64                                         
  perl-Mozilla-CA-20240313-1.fc41.noarch                                        
  perl-Net-SSLeay-1.94-3.fc40.x86_64                                            
  perl-POSIX-2.13-507.fc41.x86_64                                               
  perl-PathTools-3.89-502.fc40.x86_64                                           
  perl-Pod-Escapes-1:1.07-503.fc40.noarch                                       
  perl-Pod-Perldoc-3.28.01-503.fc40.noarch                                      
  perl-Pod-Simple-1:3.45-6.fc40.noarch                                          
  perl-Pod-Usage-4:2.03-504.fc41.noarch                                         
  perl-Scalar-List-Utils-5:1.63-503.fc40.x86_64                                 
  perl-SelectSaver-1.02-507.fc41.noarch                                         
  perl-Socket-4:2.038-1.fc41.x86_64                                             
  perl-Storable-1:3.32-502.fc40.x86_64                                          
  perl-Symbol-1.09-507.fc41.noarch                                              
  perl-Term-ANSIColor-5.01-504.fc40.noarch                                      
  perl-Term-Cap-1.18-503.fc40.noarch                                            
  perl-Text-ParseWords-3.31-502.fc40.noarch                                     
  perl-Text-Tabs+Wrap-2024.001-1.fc41.noarch                                    
  perl-Thread-Queue-3.14-503.fc40.noarch                                        
  perl-Time-Local-2:1.350-5.fc40.noarch                                         
  perl-URI-5.28-1.fc41.noarch                                                   
  perl-base-2.27-507.fc41.noarch                                                
  perl-constant-1.33-503.fc40.noarch                                            
  perl-generators-1.16-5.fc40.noarch                                            
  perl-if-0.61.000-507.fc41.noarch                                              
  perl-interpreter-4:5.38.2-507.fc41.x86_64                                     
  perl-libnet-3.15-503.fc40.noarch                                              
  perl-libs-4:5.38.2-507.fc41.x86_64                                            
  perl-locale-1.10-507.fc41.noarch                                              
  perl-macros-4:5.38.2-507.fc41.noarch                                          
  perl-mro-1.28-507.fc41.x86_64                                                 
  perl-overload-1.37-507.fc41.noarch                                            
  perl-overloading-0.02-507.fc41.noarch                                         
  perl-parent-1:0.241-502.fc40.noarch                                           
  perl-podlators-1:5.01-502.fc40.noarch                                         
  perl-threads-1:2.36-503.fc40.x86_64                                           
  perl-threads-shared-1.68-502.fc40.x86_64                                      
  perl-vars-1.05-507.fc41.noarch                                                
  python-pip-wheel-24.0-2.fc41.noarch                                           
  python3-3.12.3-2.fc41.x86_64                                                  
  python3-libs-3.12.3-2.fc41.x86_64                                             
  python3-numpy-1:1.26.4-4.fc41.x86_64                                          
  tzdata-2024a-8.fc41.noarch                                                    
  zlib-ng-compat-devel-2.1.6-4.fc41.x86_64                                      

Complete!
Finish: build setup for mmseq-1.0.11-19.fc41.src.rpm
Start: rpmbuild mmseq-1.0.11-19.fc41.src.rpm
Building target platforms: x86_64
Building for target x86_64
setting SOURCE_DATE_EPOCH=1706140800
Executing(%mkbuilddir): /bin/sh -e /var/tmp/rpm-tmp.Zqe4AD
+ umask 022
+ cd /builddir/build/BUILD/mmseq-1.0.11-build
+ test -d /builddir/build/BUILD/mmseq-1.0.11-build
+ /usr/bin/chmod -Rf a+rX,u+w,g-w,o-w /builddir/build/BUILD/mmseq-1.0.11-build
+ /usr/bin/rm -rf /builddir/build/BUILD/mmseq-1.0.11-build
+ /usr/bin/mkdir -p /builddir/build/BUILD/mmseq-1.0.11-build
+ /usr/bin/mkdir -p /builddir/build/BUILD/mmseq-1.0.11-build/SPECPARTS
+ RPM_EC=0
++ jobs -p
+ exit 0
Executing(%prep): /bin/sh -e /var/tmp/rpm-tmp.oS54C4
+ umask 022
+ cd /builddir/build/BUILD/mmseq-1.0.11-build
+ cd /builddir/build/BUILD/mmseq-1.0.11-build
+ rm -rf mmseq-1.0.11
+ /usr/lib/rpm/rpmuncompress -x /builddir/build/SOURCES/1.0.11.zip
+ STATUS=0
+ '[' 0 -ne 0 ']'
+ cd mmseq-1.0.11
+ /usr/bin/chmod -Rf a+rX,u+w,g-w,o-w .
Patch #2 (mmseq-zlib.patch):
+ echo 'Patch #2 (mmseq-zlib.patch):'
+ /usr/bin/patch --no-backup-if-mismatch -f -p1 -b --suffix .mmseq-zlib.patch --fuzz=0
patching file src/Makefile
+ rm -f bin/offsetGTF-linux bin/postdiff-linux
+ sed -e s/-lblas/-lflexiblas/g -e s/-llapack/-lflexiblas/g -i src/Makefile
+ RPM_EC=0
++ jobs -p
+ exit 0
Executing(%build): /bin/sh -e /var/tmp/rpm-tmp.0i8HmG
+ umask 022
+ cd /builddir/build/BUILD/mmseq-1.0.11-build
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ export CFLAGS
+ CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ export CXXFLAGS
+ FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules '
+ export FFLAGS
+ FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules '
+ export FCFLAGS
+ VALAFLAGS=-g
+ export VALAFLAGS
+ RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none -Cforce-frame-pointers=yes -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn'
+ export RUSTFLAGS
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed  -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ export LDFLAGS
+ LT_SYS_LIBRARY_PATH=/usr/lib64:
+ export LT_SYS_LIBRARY_PATH
+ CC=gcc
+ export CC
+ CXX=g++
+ export CXX
+ cd mmseq-1.0.11
+ cd src
+ make -j2 'CXXFLAGS=-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer'
g++ -O3 -c sokal.cc
g++ -fopenmp -O3 -c uh.cpp 
g++ -DVERSION=1.0.11 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fopenmp -O3 hitsio.cpp hitsio.hpp -c hitsio.cpp
gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer    -c -o fasta.o fasta.c
g++ -DVERSION=1.0.11 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -O3 offsetGTF.cpp -o ../bin/offsetGTF
offsetGTF.cpp: In function ‘int main(int, char**)’:
offsetGTF.cpp:115:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  115 |       while(gff_ind < gff_positions[chrom].size()) {
      |             ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
offsetGTF.cpp:117:57: warning: comparison of integer expressions of different signedness: ‘std::__cxx11::basic_string<char>::size_type’ {aka ‘long unsigned int’} and ‘__gnu_cxx::__alloc_traits<std::allocator<int>, int>::value_type’ {aka ‘int’} [-Wsign-compare]
  117 |               pos + tokens[3].size() - tokens[4].size() >= gff_positions[chrom][gff_ind]) {
offsetGTF.cpp:114:11: warning: unused variable ‘curoff’ [-Wunused-variable]
  114 |       int curoff=offset;
      |           ^~~~~~
offsetGTF.cpp:150:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  150 |       while(gff_ind < gff_positions[prevchrom].size()) {
      |             ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
offsetGTF.cpp:163:53: warning: comparison of integer expressions of different signedness: ‘std::__cxx11::basic_string<char>::size_type’ {aka ‘long unsigned int’} and ‘__gnu_cxx::__alloc_traits<std::allocator<int>, int>::value_type’ {aka ‘int’} [-Wsign-compare]
  163 |           pos + tokens[3].size() - tokens[4].size() >= gff_positions[chrom][gff_ind]) {
offsetGTF.cpp:177:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  177 |     while(gff_ind < gff_positions[chrom].size() && gff_positions[chrom][gff_ind] <= pos) {
      |           ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
offsetGTF.cpp:235:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  235 |     for(int i=5; i < tokens.size(); i++) {
      |                  ~~^~~~~~~~~~~~~~~
offsetGTF.cpp:237:12: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  237 |       if(i < tokens.size()-1) {
      |          ~~^~~~~~~~~~~~~~~~~
offsetGTF.cpp:108:7: warning: unused variable ‘gff_pos’ [-Wunused-variable]
  108 |   int gff_pos= -1;
      |       ^~~~~~~
hitsio.cpp: In member function ‘void HitsfileWriter::writeHeaderSchema0()’:
hitsio.cpp:163:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  163 |         for(int i = 0; i < transcriptName.size(); i++) {
      |                        ~~^~~~~~~~~~~~~~~~~~~~~~~
hitsio.cpp: In member function ‘void HitsfileWriter::writeReadMapRecordSchema0()’:
hitsio.cpp:184:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  184 |         for(int i = 0; i < currentReadTranscripts.size(); i++) {
      |                        ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
hitsio.cpp: In member function ‘void HitsfileWriter::writeHeaderSchema1()’:
hitsio.cpp:24:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
   24 |         if (VAL > numeric_limits<uint32_t>::max()) { \
      |                 ^
hitsio.cpp:191:9: note: in expansion of macro ‘WRITE_UINT’
  191 |         WRITE_UINT(ofs, hitsfileSchema);
      |         ^~~~~~~~~~
hitsio.cpp:193:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  193 |         for(int i = 0; i < transcriptName.size(); i++) {
      |                        ~~^~~~~~~~~~~~~~~~~~~~~~~
hitsio.cpp:24:17: warning: comparison of integer expressions of different signedness: ‘std::map<std::__cxx11::basic_string<char>, int>::mapped_type’ {aka ‘int’} and ‘unsigned int’ [-Wsign-compare]
   24 |         if (VAL > numeric_limits<uint32_t>::max()) { \
hitsio.cpp:196:17: note: in expansion of macro ‘WRITE_UINT’
  196 |                 WRITE_UINT(ofs, transcriptTrueLength[transcriptName[i] ])
      |                 ^~~~~~~~~~
hitsio.cpp: In member function ‘void HitsfileWriter::writeReadMapRecordSchema1()’:
hitsio.cpp:236:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  236 |         for(int i = 0; i < currentReadTranscripts.size(); i++) {
      |                        ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
hitsio.cpp: In member function ‘void HitsfileReader::readHeaderSchema1(std::vector<std::__cxx11::basic_string<char> >*, std::map<std::__cxx11::basic_string<char>, double>*, std::map<std::__cxx11::basic_string<char>, int>*, std::map<std::__cxx11::basic_string<char>, std::vector<std::__cxx11::basic_string<char> > >*, std::vector<std::vector<std::__cxx11::basic_string<char> > >*)’:
hitsio.cpp:356:16: warning: unused variable ‘nextStrLen’ [-Wunused-variable]
  356 |         size_t nextStrLen;
      |                ^~~~~~~~~~
hitsio.cpp: In member function ‘bool HitsfileReader::readReadMapRecordTranscriptID(std::string&)’:
hitsio.cpp:447:1: warning: control reaches end of non-void function [-Wreturn-type]
  447 | }
      | ^
g++ -DVERSION=1.0.11 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -O3 t2g_hits.cpp -o ../bin/t2g_hits
t2g_hits.cpp: In function ‘int main(int, char**)’:
t2g_hits.cpp:90:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   90 |         for(int i=2; i < tokens.size(); i++) {
      |                      ~~^~~~~~~~~~~~~~~
t2g_hits.cpp:112:13: warning: ignoring return value of ‘_FIter std::unique(_FIter, _FIter) [with _FIter = __gnu_cxx::__normal_iterator<__cxx11::basic_string<char>*, vector<__cxx11::basic_string<char> > >]’, declared with attribute ‘nodiscard’ [-Wunused-result]
  112 |       unique(comb.begin(), comb.end());
      |       ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/algorithm:61,
                 from t2g_hits.cpp:27:
/usr/include/c++/14/bits/stl_algo.h:891:5: note: declared here
  891 |     unique(_ForwardIterator __first, _ForwardIterator __last)
      |     ^~~~~~
g++ -DVERSION=1.0.11 -DARMA_64BIT_WORD -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fopenmp -O3 uh.o sokal.o mmcollapse.cpp -o ../bin/mmcollapse -lgsl -lgslcblas -lboost_regex -lhts -lboost_iostreams -lflexiblas -lflexiblas -Wl,--as-needed -lz -lgfortran
mmcollapse.cpp: In function ‘void get_unidentifiable_transcripts(std::string, std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >&, std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >&, std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >&, std::map<std::__cxx11::basic_string<char>, std::map<std::__cxx11::basic_string<char>, double> >&, std::map<std::__cxx11::basic_string<char>, std::map<std::__cxx11::basic_string<char>, double> >&, std::map<std::__cxx11::basic_string<char>, std::map<std::__cxx11::basic_string<char>, double> >&, std::map<std::__cxx11::basic_string<char>, int>&, std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >&, std::map<std::__cxx11::basic_string<char>, bool>&)’:
mmcollapse.cpp:158:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  158 |   for(int i=0; i < tokens.size(); i++) {
      |                ~~^~~~~~~~~~~~~~~
mmcollapse.cpp:213:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  213 |     for(int i=0; i < tokens2.size(); i++) isIdent[tokens2[i]]=1;
      |                  ~~^~~~~~~~~~~~~~~~
mmcollapse.cpp:259:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  259 |   for(int i=0; i < tokens.size(); i++) {
      |                ~~^~~~~~~~~~~~~~~
mmcollapse.cpp: In function ‘void collapse(arma::cube&, std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >&, std::map<std::__cxx11::basic_string<char>, int>&, std::vector<int, std::allocator<int> >)’:
mmcollapse.cpp:400:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
  400 |   for(int s=0; s < R.n_slices; s++) {
      |                ~~^~~~~~~~~~~~
mmcollapse.cpp:401:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  401 |     for(int t=0; t < candidates.size(); t++) {
      |                  ~~^~~~~~~~~~~~~~~~~~~
mmcollapse.cpp:402:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int, std::allocator<int> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  402 |       for(int j=1; j < indexes.size(); j++) {
      |                    ~~^~~~~~~~~~~~~~~~
mmcollapse.cpp:414:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int, std::allocator<int> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  414 |     for(int j=1; j < indexes.size(); j++) {
      |                  ~~^~~~~~~~~~~~~~~~
mmcollapse.cpp:417:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
  417 |       for(int i=0; i < R.n_cols; i++) {
      |                    ~~^~~~~~~~~~
mmcollapse.cpp:426:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int, std::allocator<int> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  426 |   for(int i=0; i < indexes.size(); i++) {
      |                ~~^~~~~~~~~~~~~~~~
mmcollapse.cpp:431:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  431 |   for(int i=1; i < tset.size(); i++) {
      |                ~~^~~~~~~~~~~~~
mmcollapse.cpp:437:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int, std::allocator<int> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  437 |   for(int i=1; i < indexes.size(); i++) {
      |                ~~^~~~~~~~~~~~~~~~
mmcollapse.cpp: In function ‘std::map<int, int> join_traces(arma::mat&, std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >&, std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >)’:
mmcollapse.cpp:445:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  445 |   for(int t=0; t < allnames.size(); t++) tmap[allnames[t]]=t;
      |                ~~^~~~~~~~~~~~~~~~~
mmcollapse.cpp:452:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  452 |   for(int c=0; c < candidates.size(); c++) {
      |                ~~^~~~~~~~~~~~~~~~~~~
mmcollapse.cpp:456:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  456 |     for(int t=0; t < tokens.size(); t++) {
      |                  ~~^~~~~~~~~~~~~~~
mmcollapse.cpp:464:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int, std::allocator<int> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  464 |     for(int t=1; t < indexes.size(); t++) {
      |                  ~~^~~~~~~~~~~~~~~~
mmcollapse.cpp:469:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int, std::allocator<int> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  469 |     for(int t=1; t < indexes.size(); t++) {
      |                  ~~^~~~~~~~~~~~~~~~
mmcollapse.cpp:476:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int, std::allocator<int> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  476 |   for(int i=0; i < toshed.size(); i++) {
      |                ~~^~~~~~~~~~~~~~~
mmcollapse.cpp: In function ‘void mean_corrs(const arma::cube&, const arma::umat&, arma::mat&, arma::mat&, std::vector<int, std::allocator<int> >, std::vector<int, std::allocator<int> >, double)’:
mmcollapse.cpp:486:21: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
  486 |     for(int v= 0; v < R.n_rows; v++) {
      |                   ~~^~~~~~~~~~
mmcollapse.cpp:492:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘arma::uword’ {aka ‘long long unsigned int’} [-Wsign-compare]
  492 |       for(int i=0; i < u.size(); i++) {
      |                    ~~^~~~~~~~~~
mmcollapse.cpp: In function ‘void get_corrs(arma::cube&, arma::mat&, const std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >&, std::map<std::__cxx11::basic_string<char>, int>&)’:
mmcollapse.cpp:519:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  519 |   for(int s=0; s < basenames.size(); s++) {
      |                ~~^~~~~~~~~~~~~~~~~~
mmcollapse.cpp:543:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  543 |         for(int t=0; t < tokens.size(); t++) {
      |                      ~~^~~~~~~~~~~~~~~
mmcollapse.cpp: In function ‘int main(int, char**)’:
mmcollapse.cpp:632:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  632 |   for(int i=1; i < basenames.size(); i++) {
      |                ~~^~~~~~~~~~~~~~~~~~
mmcollapse.cpp:691:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  691 |   for(int s=0; s < basenames.size(); s++) {
      |                ~~^~~~~~~~~~~~~~~~~~
mmcollapse.cpp:707:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  707 |   for(int i=0; i < candidates.size(); i++) ts.push_back(i);
      |                ~~^~~~~~~~~~~~~~~~~~~
mmcollapse.cpp:732:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  732 |     for(int i=0 ;i < maxcorrs.size(); i++) {
      |                  ~~^~~~~~~~~~~~~~~~~
mmcollapse.cpp:738:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  738 |     for(int i=0 ;i < mincorrs.size(); i++) {
      |                  ~~^~~~~~~~~~~~~~~~~
mmcollapse.cpp:802:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  802 |         for(int i=0 ;i < maxcorrs.size(); i++) {
      |                      ~~^~~~~~~~~~~~~~~~~
mmcollapse.cpp:808:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  808 |         for(int i=0 ;i < mincorrs.size(); i++) {
      |                      ~~^~~~~~~~~~~~~~~~~
mmcollapse.cpp:827:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  827 |   for(int s=0; s < basenames.size(); s++) {
      |                ~~^~~~~~~~~~~~~~~~~~
mmcollapse.cpp:852:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  852 |       for(int t=0; t < tokens.size(); t++) {
      |                    ~~^~~~~~~~~~~~~~~
mmcollapse.cpp:882:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  882 |       for(int t=0; t < tokens2.size(); t++) {
      |                    ~~^~~~~~~~~~~~~~~~
mmcollapse.cpp:934:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
  934 |     for(int t=0; t < M.n_cols; t++) {
      |                  ~~^~~~~~~~~~
mmcollapse.cpp:963:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  963 |     for(int i=1; i < tokens2.size(); i++) {
      |                  ~~^~~~~~~~~~~~~~~~
mmcollapse.cpp:976:21: warning: comparison of integer expressions of different signedness: ‘boost::numeric::ublas::compressed_matrix<bool>::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
  976 |       if(MM.size1() < i+1 ) factor1=2;
      |          ~~~~~~~~~~~^~~~~
mmcollapse.cpp:977:21: warning: comparison of integer expressions of different signedness: ‘boost::numeric::ublas::compressed_matrix<bool>::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
  977 |       if(MM.size2() < j+1 ) factor2=2;
      |          ~~~~~~~~~~~^~~~~
mmcollapse.cpp:1010:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1010 |     for(int t=0; t < ids.size(); t++) {
      |                  ~~^~~~~~~~~~~~
mmcollapse.cpp:1083:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1083 |     for(int i=0; i < ids.size(); i++) {
      |                  ~~^~~~~~~~~~~~
mmcollapse.cpp:1092:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
 1092 |     for(int v = 0; v < M.n_cols; v++) {
      |                    ~~^~~~~~~~~~
mmcollapse.cpp:840:9: warning: unused variable ‘isident’ [-Wunused-variable]
  840 |     int isident=0;
      |         ^~~~~~~
hitsio.cpp: In member function ‘void HitsfileWriter::writeHeaderSchema0()’:
hitsio.cpp:163:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  163 |         for(int i = 0; i < transcriptName.size(); i++) {
      |                        ~~^~~~~~~~~~~~~~~~~~~~~~~
hitsio.cpp: In member function ‘void HitsfileWriter::writeReadMapRecordSchema0()’:
hitsio.cpp:184:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  184 |         for(int i = 0; i < currentReadTranscripts.size(); i++) {
      |                        ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
hitsio.cpp: In member function ‘void HitsfileWriter::writeHeaderSchema1()’:
hitsio.cpp:24:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
   24 |         if (VAL > numeric_limits<uint32_t>::max()) { \
      |                 ^
hitsio.cpp:191:9: note: in expansion of macro ‘WRITE_UINT’
  191 |         WRITE_UINT(ofs, hitsfileSchema);
      |         ^~~~~~~~~~
hitsio.cpp:193:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  193 |         for(int i = 0; i < transcriptName.size(); i++) {
      |                        ~~^~~~~~~~~~~~~~~~~~~~~~~
hitsio.cpp:24:17: warning: comparison of integer expressions of different signedness: ‘std::map<std::__cxx11::basic_string<char>, int>::mapped_type’ {aka ‘int’} and ‘unsigned int’ [-Wsign-compare]
   24 |         if (VAL > numeric_limits<uint32_t>::max()) { \
hitsio.cpp:196:17: note: in expansion of macro ‘WRITE_UINT’
  196 |                 WRITE_UINT(ofs, transcriptTrueLength[transcriptName[i] ])
      |                 ^~~~~~~~~~
hitsio.cpp: In member function ‘void HitsfileWriter::writeReadMapRecordSchema1()’:
hitsio.cpp:236:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  236 |         for(int i = 0; i < currentReadTranscripts.size(); i++) {
      |                        ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
hitsio.cpp: In member function ‘void HitsfileReader::readHeaderSchema1(std::vector<std::__cxx11::basic_string<char> >*, std::map<std::__cxx11::basic_string<char>, double>*, std::map<std::__cxx11::basic_string<char>, int>*, std::map<std::__cxx11::basic_string<char>, std::vector<std::__cxx11::basic_string<char> > >*, std::vector<std::vector<std::__cxx11::basic_string<char> > >*)’:
hitsio.cpp:356:16: warning: unused variable ‘nextStrLen’ [-Wunused-variable]
  356 |         size_t nextStrLen;
      |                ^~~~~~~~~~
hitsio.cpp: In member function ‘bool HitsfileReader::readReadMapRecordTranscriptID(std::string&)’:
hitsio.cpp:447:1: warning: control reaches end of non-void function [-Wreturn-type]
  447 | }
      | ^
g++ -DVERSION=1.0.11 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fopenmp -O2 bms.cpp bms.hpp -c bms.cpp
bms.cpp: In member function ‘arma::Col<int> BMS::m2v(arma::Mat<double>)’:
bms.cpp:36:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
   36 |   for(int i=0; i < P.n_cols; i++) {
      |                ~~^~~~~~~~~~
bms.cpp:37:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
   37 |     for(int j=0; j < P.n_rows; j++) {
      |                  ~~^~~~~~~~~~
bms.cpp: In member function ‘std::vector<double> BMS::meanvar(arma::Col<double>)’:
bms.cpp:76:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
   76 |   for(int i=0;i < v.n_elem; i++) {
      |               ~~^~~~~~~~~~
bms.cpp: In member function ‘void BMS::print(bool)’:
bms.cpp:93:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
   93 |   for(int feature=0; feature < y->n_rows; feature++) {
      |                      ~~~~~~~~^~~~~~~~~~~
bms.cpp:97:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
   97 |       for(int i=0; i < M.n_cols; i++) {
      |                    ~~^~~~~~~~~~
bms.cpp:102:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
  102 |       for(int l=0; l < P[model].n_cols; l++) {
      |                    ~~^~~~~~~~~~~~~~~~~
bms.cpp: In member function ‘void BMS::printtune(int)’:
bms.cpp:132:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
  132 |   for(int feature=0; feature < y->n_rows; feature++) {
      |                      ~~~~~~~~^~~~~~~~~~~
bms.cpp: In member function ‘void BMS::set_pseudoprior_alpha()’:
bms.cpp:185:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
  185 |     for(int j=0; j < y->n_rows; j++) {
      |                  ~~^~~~~~~~~~~
bms.cpp: In member function ‘void BMS::set_pseudoprior_beta()’:
bms.cpp:253:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
  253 |   for(int j=0; j < y->n_rows; j++) {
      |                ~~^~~~~~~~~~~
bms.cpp:255:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
  255 |       for(int b=0; b < M.n_cols; b++) {
      |                    ~~^~~~~~~~~~
bms.cpp: In member function ‘void BMS::set_pseudoprior_eta()’:
bms.cpp:332:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
  332 |   for(int j=0; j < y->n_rows; j++) {
      |                ~~^~~~~~~~~~~
bms.cpp:334:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
  334 |       for(int c=0; c < P[model].n_cols; c++) {
      |                    ~~^~~~~~~~~~~~~~~~~
bms.cpp: In member function ‘void BMS::set_pseudoprior_sigmasq()’:
bms.cpp:415:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
  415 |   for(int j=0; j < y->n_rows; j++) {
      |                ~~^~~~~~~~~~~
bms.cpp: In member function ‘void BMS::set_pseudoprior_lambda()’:
bms.cpp:504:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
  504 |   for(int j=0; j < y->n_rows; j++) {
      |                ~~^~~~~~~~~~~
bms.cpp:506:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
  506 |       for(int l=0; l < P[model].n_cols; l++) {
      |                    ~~^~~~~~~~~~~~~~~~~
bms.cpp: In member function ‘void BMS::set_pseudoprior_rho()’:
bms.cpp:559:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
  559 |     for(int j=0; j < y->n_rows; j++) {
      |                  ~~^~~~~~~~~~~
bms.cpp: In member function ‘void BMS::copy_pseudo()’:
bms.cpp:582:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
  582 |   for(int j=0; j < y->n_rows; j++) {
      |                ~~^~~~~~~~~~~
bms.cpp:585:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
  585 |     for(int c=0; c < P[0].n_cols; c++) {
      |                  ~~^~~~~~~~~~~~~
bms.cpp: In member function ‘void BMS::update_alpha(int, int, bool)’:
bms.cpp:603:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
  603 |     for(int j=0; j < y->n_cols; j++) {
      |                  ~~^~~~~~~~~~~
bms.cpp:610:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
  610 |     for(int i=0; i < y->n_cols; i++) {
      |                  ~~^~~~~~~~~~~
bms.cpp: In member function ‘void BMS::update_beta(int, int, bool)’:
bms.cpp:631:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
  631 |     for(int j=0; j < y->n_cols; j++) {
      |                  ~~^~~~~~~~~~~
bms.cpp:638:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
  638 |     for(int i=0; i < M.n_cols; i++) {
      |                  ~~^~~~~~~~~~
bms.cpp:646:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
  646 |     for(int i=0; i < M.n_cols; i++) {
      |                  ~~^~~~~~~~~~
bms.cpp:651:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
  651 |     for(int i=0; i < M.n_cols; i++) {
      |                  ~~^~~~~~~~~~
bms.cpp: In member function ‘void BMS::update_eta(int, int, bool)’:
bms.cpp:663:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
  663 |     for(int l=0; l < P[model].n_cols; l++) {
      |                  ~~^~~~~~~~~~~~~~~~~
bms.cpp:666:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
  666 |       for(int i=0; i < y->n_cols; i++) {
      |                    ~~^~~~~~~~~~~
bms.cpp:673:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
  673 |       for(int i=0; i < y->n_cols; i++) {
      |                    ~~^~~~~~~~~~~
bms.cpp:681:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
  681 |     for(int l=0; l < P[model].n_cols; l++) {
      |                  ~~^~~~~~~~~~~~~~~~~
bms.cpp:686:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
  686 |     for(int l=0; l < P[model].n_cols; l++) {
      |                  ~~^~~~~~~~~~~~~~~~~
bms.cpp: In member function ‘void BMS::update_lambda(int, int, bool)’:
bms.cpp:699:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
  699 |     for(int l=0; l < P[model].n_cols; l++) {
      |                  ~~^~~~~~~~~~~~~~~~~
bms.cpp:704:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
  704 |     for(int l=0; l < P[model].n_cols; l++) {
      |                  ~~^~~~~~~~~~~~~~~~~
bms.cpp:711:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
  711 |     for(int l=0; l < P[model].n_cols; l++) {
      |                  ~~^~~~~~~~~~~~~~~~~
bms.cpp: In member function ‘void BMS::update_sigmasq(int, int, bool, bool)’:
bms.cpp:729:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
  729 |     for(int i=0; i < y->n_cols; i++) {
      |                  ~~^~~~~~~~~~~
bms.cpp:740:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
  740 |     for(int i=0; i < y->n_cols; i++) {
      |                  ~~^~~~~~~~~~~
bms.cpp:751:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
  751 |         for(int i=0; i < y->n_cols; i++) {
      |                      ~~^~~~~~~~~~~
bms.cpp:763:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
  763 |         for(int i=0; i < y->n_cols; i++) {
      |                      ~~^~~~~~~~~~~
bms.cpp: In member function ‘void BMS::update_sigmasq_RW(int, int, bool, bool)’:
bms.cpp:877:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
  877 |     for(int i=0; i < y->n_cols; i++) {
      |                  ~~^~~~~~~~~~~
bms.cpp: In member function ‘double BMS::log_target_posterior(int, int)’:
bms.cpp:931:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
  931 |   for(int i=0; i < y->n_cols; i++) {
      |                ~~^~~~~~~~~~~
bms.cpp:940:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
  940 |     for(int j=0; j < M.n_cols; j++) {
      |                  ~~^~~~~~~~~~
bms.cpp:947:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
  947 |     for(int l=0; l < P[model].n_cols; l++) {
      |                  ~~^~~~~~~~~~~~~~~~~
bms.cpp: In member function ‘double BMS::log_target_pseudo(int, int)’:
bms.cpp:968:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
  968 |     for(int l=0; l < M.n_cols; l++) {
      |                  ~~^~~~~~~~~~
bms.cpp:974:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
  974 |     for(int l=0; l < P[model].n_cols; l++) {
      |                  ~~^~~~~~~~~~~~~~~~~
bms.cpp: In member function ‘void BMS::print_pseudo()’:
bms.cpp:1086:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
 1086 |     for(int l=0; l < M.n_cols; l++) {
      |                  ~~^~~~~~~~~~
bms.cpp:1089:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
 1089 |     for(int l=0; l < P[model].n_cols; l++) {
      |                  ~~^~~~~~~~~~~~~~~~~
bms.cpp:1100:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
 1100 |   for(int i=0; i < y->n_rows; i++) {
      |                ~~^~~~~~~~~~~
bms.cpp:1103:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
 1103 |       for(int l=0; l < M.n_cols; l++) {
      |                    ~~^~~~~~~~~~
bms.cpp:1106:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
 1106 |       for(int l=0; l < P[model].n_cols; l++) {
      |                    ~~^~~~~~~~~~~~~~~~~
bms.cpp: In constructor ‘BMS::BMS(const arma::Mat<double>*, const arma::Mat<double>&, arma::Mat<double>, arma::Mat<double>, arma::Mat<double>, arma::Mat<int>, double, double, double, std::string, gsl_rng**, int, bool)’:
bms.cpp:1188:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
 1188 |     for(int i=0; i < y->n_cols; i++) {
      |                  ~~^~~~~~~~~~~
bms.cpp:1192:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int, std::allocator<int> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1192 |         if(C(i,model)+1 > _n.size()) {
      |            ~~~~~~~~~~~~~^~~~~~~~~~~
bms.cpp: In member function ‘void BMS::initialise_streams(std::string)’:
bms.cpp:1348:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
 1348 |   for(int i=0; i < M.n_cols; i++) {
      |                ~~^~~~~~~~~~
bms.cpp:1354:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
 1354 |   for(int i=0; i < M.n_cols; i++) {
      |                ~~^~~~~~~~~~
bms.cpp:1360:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
 1360 |   for(int i=0; i < P[0].n_cols; i++) {
      |                ~~^~~~~~~~~~~~~
bms.cpp:1366:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
 1366 |   for(int i=0; i < P[1].n_cols; i++) {
      |                ~~^~~~~~~~~~~~~
bms.cpp:1372:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
 1372 |   for(int i=0; i < P[0].n_cols; i++) {
      |                ~~^~~~~~~~~~~~~
bms.cpp:1378:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
 1378 |   for(int i=0; i < P[1].n_cols; i++) {
      |                ~~^~~~~~~~~~~~~
g++ -DVERSION=1.0.11 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fopenmp -O3 sokal.o uh.o hitsio.o mmseq.cpp -o ../bin/mmseq -lgsl -lgslcblas -lboost_regex -lhts -lboost_iostreams -lflexiblas -lflexiblas -Wl,--as-needed -lz -lgfortran
mmseq.cpp: In function ‘std::vector<double> meanvar(std::vector<double>, double, double)’:
mmseq.cpp:130:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  130 |   for(int i=0;i < v.size(); i++) {
      |               ~~^~~~~~~~~~
mmseq.cpp: In function ‘int main(int, char**)’:
mmseq.cpp:244:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  244 |       for(int i=0; i < tokens.size(); i++) {
      |                    ~~^~~~~~~~~~~~~~~
mmseq.cpp:423:20: warning: comparison of integer expressions of different signedness: ‘boost::numeric::ublas::compressed_matrix<bool>::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
  423 |       if(M.size1() < m ) factor1=2;
      |          ~~~~~~~~~~^~~
mmseq.cpp:424:20: warning: comparison of integer expressions of different signedness: ‘boost::numeric::ublas::compressed_matrix<bool>::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
  424 |       if(M.size2() < n ) factor2=2;
      |          ~~~~~~~~~~^~~
mmseq.cpp:594:23: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
  594 |   for(unsigned t=0; t < n; t++)  {
      |                     ~~^~~
mmseq.cpp:736:25: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
  736 |     for(unsigned t=0; t < n; t++)
      |                       ~~^~~
mmseq.cpp:765:27: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
  765 |       for(unsigned t=0; t < n; t++)
      |                         ~~^~~
mmseq.cpp:774:11: warning: unused variable ‘threadid’ [-Wunused-variable]
  774 |       int threadid=OMP_GET_THREAD_NUM;
      |           ^~~~~~~~
mmseq.cpp:829:23: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
  829 |   for(unsigned t=0; t < n; t++)
      |                     ~~^~~
mmseq.cpp:912:27: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
  912 |       for(unsigned t=0; t < n; t++) {
      |                         ~~^~~
mmseq.cpp:940:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<std::__cxx11::basic_string<char> > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  940 |   for(int i=0; i < identical_transcripts.size() * trace_length; i++) mu_trace_identical[i]=0;
      |                ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
mmseq.cpp:961:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::map<std::__cxx11::basic_string<char>, std::vector<std::__cxx11::basic_string<char> > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  961 |   for(int i=0; i < gene2transcripts.size() * trace_length; i++) mu_trace_gene[i]=0;
      |                ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
mmseq.cpp:1098:23: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
 1098 |   for(unsigned t=0; t < n; t++) gofs << indexSid[t] << " ";
      |                     ~~^~~
mmseq.cpp:1112:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1112 |   for(int i=0; i < percentiles.size(); i++) {
      |                ~~^~~~~~~~~~~~~~~~~~~~
mmseq.cpp:1136:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1136 |     for(int j=0; j < percentiles.size(); j++) {
      |                  ~~^~~~~~~~~~~~~~~~~~~~
mmseq.cpp:1144:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1144 |     for(int j=0; j < percentiles.size(); j++) {
      |                  ~~^~~~~~~~~~~~~~~~~~~~
mmseq.cpp:1149:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<std::__cxx11::basic_string<char> > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1149 |   for(int i=0;i < identical_transcripts.size(); i++) {
      |               ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
mmseq.cpp:1156:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1156 |     for(int j=0; j < percentiles.size(); j++) {
      |                  ~~^~~~~~~~~~~~~~~~~~~~
mmseq.cpp:1161:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::map<std::__cxx11::basic_string<char>, std::vector<std::__cxx11::basic_string<char> > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1161 |   for(int i=0;i < gene2transcripts.size(); i++) {
      |               ~~^~~~~~~~~~~~~~~~~~~~~~~~~
mmseq.cpp:1168:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1168 |     for(int j=0; j < percentiles.size(); j++) {
      |                  ~~^~~~~~~~~~~~~~~~~~~~
mmseq.cpp:1179:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1179 |     for(int j=0; j < percentiles.size(); j++) {
      |                  ~~^~~~~~~~~~~~~~~~~~~~
mmseq.cpp:1189:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1189 |     for(int j=0; j < percentiles.size(); j++) {
      |                  ~~^~~~~~~~~~~~~~~~~~~~
mmseq.cpp:1208:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<std::__cxx11::basic_string<char> > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1208 |     for(int t=0; t < identical_transcripts.size() ; t++) {
      |                  ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
mmseq.cpp:1212:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::map<std::__cxx11::basic_string<char>, std::vector<std::__cxx11::basic_string<char> > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1212 |     for(int t=0; t < gene2transcripts.size(); t++){
      |                  ~~^~~~~~~~~~~~~~~~~~~~~~~~~
mmseq.cpp:1226:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<std::__cxx11::basic_string<char> > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1226 |   for(int i=0; i < identical_transcripts.size() ; i++) meanmu_identical[i] /= trace_length;
      |                ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
mmseq.cpp:1227:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::map<std::__cxx11::basic_string<char>, std::vector<std::__cxx11::basic_string<char> > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1227 |   for(int i=0; i < gene2transcripts.size(); i++) meanmu_gene[i]/= trace_length;
      |                ~~^~~~~~~~~~~~~~~~~~~~~~~~~
mmseq.cpp:1330:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::vector<std::__cxx11::basic_string<char> > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1330 |   for(int t=0; t < identical_transcripts.size(); t++) {
      |                ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
mmseq.cpp:1349:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::map<std::__cxx11::basic_string<char>, std::vector<std::__cxx11::basic_string<char> > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1349 |   for(int g=0; g < gene2transcripts.size(); g++) {
      |                ~~^~~~~~~~~~~~~~~~~~~~~~~~~
mmseq.cpp:1473:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1473 |   for(int i=0; i < percentiles.size(); i++) {
      |                ~~^~~~~~~~~~~~~~~~~~~~
mmseq.cpp:1475:9: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1475 |     if(i==percentiles.size()-1) {
      |        ~^~~~~~~~~~~~~~~~~~~~~~
mmseq.cpp:1482:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1482 |   for(int i=0; i < percentiles.size(); i++) {
      |                ~~^~~~~~~~~~~~~~~~~~~~
mmseq.cpp:1484:9: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1484 |     if(i==percentiles.size()-1) {
      |        ~^~~~~~~~~~~~~~~~~~~~~~
mmseq.cpp:1506:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1506 |       for(int i=0; i < percentiles.size(); i++) {
      |                    ~~^~~~~~~~~~~~~~~~~~~~
mmseq.cpp:1508:13: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1508 |         if(i==percentiles.size()-1) {
      |            ~^~~~~~~~~~~~~~~~~~~~~~
mmseq.cpp:1514:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1514 |       for(int i=0; i < percentiles.size(); i++) {
      |                    ~~^~~~~~~~~~~~~~~~~~~~
mmseq.cpp:1516:13: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1516 |         if(i==percentiles.size()-1) {
      |            ~^~~~~~~~~~~~~~~~~~~~~~
mmseq.cpp:1536:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1536 |       for(int i=0; i < percentiles.size(); i++) {
      |                    ~~^~~~~~~~~~~~~~~~~~~~
mmseq.cpp:1538:13: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1538 |         if(i==percentiles.size()-1) {
      |            ~^~~~~~~~~~~~~~~~~~~~~~
mmseq.cpp:1544:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1544 |       for(int i=0; i < percentiles.size(); i++) {
      |                    ~~^~~~~~~~~~~~~~~~~~~~
mmseq.cpp:1546:13: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1546 |         if(i==percentiles.size()-1) {
      |            ~^~~~~~~~~~~~~~~~~~~~~~
mmseq.cpp:1560:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1560 |   for(int i=0; i < percentiles.size(); i++) {
      |                ~~^~~~~~~~~~~~~~~~~~~~
mmseq.cpp:1562:9: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1562 |     if(i==percentiles.size()-1) {
      |        ~^~~~~~~~~~~~~~~~~~~~~~
mmseq.cpp:1582:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1582 |         for(int i=0; i < percentiles.size(); i++) {
      |                      ~~^~~~~~~~~~~~~~~~~~~~
mmseq.cpp:1584:15: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1584 |           if(i==percentiles.size()-1) {
      |              ~^~~~~~~~~~~~~~~~~~~~~~
mmseq.cpp:1599:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1599 |         for(int i=0; i < percentiles.size(); i++) {
      |                      ~~^~~~~~~~~~~~~~~~~~~~
mmseq.cpp:1601:15: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1601 |           if(i==percentiles.size()-1) {
      |              ~^~~~~~~~~~~~~~~~~~~~~~
mmseq.cpp:1619:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1619 |   for(int i=0; i < percentiles.size(); i++) {
      |                ~~^~~~~~~~~~~~~~~~~~~~
mmseq.cpp:1621:9: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1621 |     if(i==percentiles.size()-1) {
      |        ~^~~~~~~~~~~~~~~~~~~~~~
mmseq.cpp:1644:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1644 |         for(int i=0; i < percentiles.size(); i++) {
      |                      ~~^~~~~~~~~~~~~~~~~~~~
mmseq.cpp:1646:15: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1646 |           if(i==percentiles.size()-1) {
      |              ~^~~~~~~~~~~~~~~~~~~~~~
mmseq.cpp:1656:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1656 |         for(int i=0; i < percentiles.size(); i++) {
      |                      ~~^~~~~~~~~~~~~~~~~~~~
mmseq.cpp:1658:15: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1658 |           if(i==percentiles.size()-1) {
      |              ~^~~~~~~~~~~~~~~~~~~~~~
mmseq.cpp:308:8: warning: unused variable ‘buf16384’ [-Wunused-variable]
  308 |   char buf16384[16384];
      |        ^~~~~~~~
mmseq.cpp:391:8: warning: variable ‘doublehit’ set but not used [-Wunused-but-set-variable]
  391 |   bool doublehit;
      |        ^~~~~~~~~
bms.cpp: In member function ‘arma::Col<int> BMS::m2v(arma::Mat<double>)’:
bms.cpp:36:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
   36 |   for(int i=0; i < P.n_cols; i++) {
      |                ~~^~~~~~~~~~
bms.cpp:37:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
   37 |     for(int j=0; j < P.n_rows; j++) {
      |                  ~~^~~~~~~~~~
bms.cpp: In member function ‘std::vector<double> BMS::meanvar(arma::Col<double>)’:
bms.cpp:76:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
   76 |   for(int i=0;i < v.n_elem; i++) {
      |               ~~^~~~~~~~~~
bms.cpp: In member function ‘void BMS::print(bool)’:
bms.cpp:93:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
   93 |   for(int feature=0; feature < y->n_rows; feature++) {
      |                      ~~~~~~~~^~~~~~~~~~~
bms.cpp:97:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
   97 |       for(int i=0; i < M.n_cols; i++) {
      |                    ~~^~~~~~~~~~
bms.cpp:102:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
  102 |       for(int l=0; l < P[model].n_cols; l++) {
      |                    ~~^~~~~~~~~~~~~~~~~
bms.cpp: In member function ‘void BMS::printtune(int)’:
bms.cpp:132:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
  132 |   for(int feature=0; feature < y->n_rows; feature++) {
      |                      ~~~~~~~~^~~~~~~~~~~
bms.cpp: In member function ‘void BMS::set_pseudoprior_alpha()’:
bms.cpp:185:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
  185 |     for(int j=0; j < y->n_rows; j++) {
      |                  ~~^~~~~~~~~~~
bms.cpp: In member function ‘void BMS::set_pseudoprior_beta()’:
bms.cpp:253:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
  253 |   for(int j=0; j < y->n_rows; j++) {
      |                ~~^~~~~~~~~~~
bms.cpp:255:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
  255 |       for(int b=0; b < M.n_cols; b++) {
      |                    ~~^~~~~~~~~~
bms.cpp: In member function ‘void BMS::set_pseudoprior_eta()’:
bms.cpp:332:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
  332 |   for(int j=0; j < y->n_rows; j++) {
      |                ~~^~~~~~~~~~~
bms.cpp:334:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
  334 |       for(int c=0; c < P[model].n_cols; c++) {
      |                    ~~^~~~~~~~~~~~~~~~~
bms.cpp: In member function ‘void BMS::set_pseudoprior_sigmasq()’:
bms.cpp:415:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
  415 |   for(int j=0; j < y->n_rows; j++) {
      |                ~~^~~~~~~~~~~
bms.cpp: In member function ‘void BMS::set_pseudoprior_lambda()’:
bms.cpp:504:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
  504 |   for(int j=0; j < y->n_rows; j++) {
      |                ~~^~~~~~~~~~~
bms.cpp:506:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
  506 |       for(int l=0; l < P[model].n_cols; l++) {
      |                    ~~^~~~~~~~~~~~~~~~~
bms.cpp: In member function ‘void BMS::set_pseudoprior_rho()’:
bms.cpp:559:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
  559 |     for(int j=0; j < y->n_rows; j++) {
      |                  ~~^~~~~~~~~~~
bms.cpp: In member function ‘void BMS::copy_pseudo()’:
bms.cpp:582:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
  582 |   for(int j=0; j < y->n_rows; j++) {
      |                ~~^~~~~~~~~~~
bms.cpp:585:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
  585 |     for(int c=0; c < P[0].n_cols; c++) {
      |                  ~~^~~~~~~~~~~~~
bms.cpp: In member function ‘void BMS::update_alpha(int, int, bool)’:
bms.cpp:603:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
  603 |     for(int j=0; j < y->n_cols; j++) {
      |                  ~~^~~~~~~~~~~
bms.cpp:610:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
  610 |     for(int i=0; i < y->n_cols; i++) {
      |                  ~~^~~~~~~~~~~
bms.cpp: In member function ‘void BMS::update_beta(int, int, bool)’:
bms.cpp:631:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
  631 |     for(int j=0; j < y->n_cols; j++) {
      |                  ~~^~~~~~~~~~~
bms.cpp:638:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
  638 |     for(int i=0; i < M.n_cols; i++) {
      |                  ~~^~~~~~~~~~
bms.cpp:646:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
  646 |     for(int i=0; i < M.n_cols; i++) {
      |                  ~~^~~~~~~~~~
bms.cpp:651:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
  651 |     for(int i=0; i < M.n_cols; i++) {
      |                  ~~^~~~~~~~~~
bms.cpp: In member function ‘void BMS::update_eta(int, int, bool)’:
bms.cpp:663:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
  663 |     for(int l=0; l < P[model].n_cols; l++) {
      |                  ~~^~~~~~~~~~~~~~~~~
bms.cpp:666:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
  666 |       for(int i=0; i < y->n_cols; i++) {
      |                    ~~^~~~~~~~~~~
bms.cpp:673:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
  673 |       for(int i=0; i < y->n_cols; i++) {
      |                    ~~^~~~~~~~~~~
bms.cpp:681:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
  681 |     for(int l=0; l < P[model].n_cols; l++) {
      |                  ~~^~~~~~~~~~~~~~~~~
bms.cpp:686:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
  686 |     for(int l=0; l < P[model].n_cols; l++) {
      |                  ~~^~~~~~~~~~~~~~~~~
bms.cpp: In member function ‘void BMS::update_lambda(int, int, bool)’:
bms.cpp:699:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
  699 |     for(int l=0; l < P[model].n_cols; l++) {
      |                  ~~^~~~~~~~~~~~~~~~~
bms.cpp:704:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
  704 |     for(int l=0; l < P[model].n_cols; l++) {
      |                  ~~^~~~~~~~~~~~~~~~~
bms.cpp:711:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
  711 |     for(int l=0; l < P[model].n_cols; l++) {
      |                  ~~^~~~~~~~~~~~~~~~~
bms.cpp: In member function ‘void BMS::update_sigmasq(int, int, bool, bool)’:
bms.cpp:729:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
  729 |     for(int i=0; i < y->n_cols; i++) {
      |                  ~~^~~~~~~~~~~
bms.cpp:740:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
  740 |     for(int i=0; i < y->n_cols; i++) {
      |                  ~~^~~~~~~~~~~
bms.cpp:751:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
  751 |         for(int i=0; i < y->n_cols; i++) {
      |                      ~~^~~~~~~~~~~
bms.cpp:763:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
  763 |         for(int i=0; i < y->n_cols; i++) {
      |                      ~~^~~~~~~~~~~
bms.cpp: In member function ‘void BMS::update_sigmasq_RW(int, int, bool, bool)’:
bms.cpp:877:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
  877 |     for(int i=0; i < y->n_cols; i++) {
      |                  ~~^~~~~~~~~~~
bms.cpp: In member function ‘double BMS::log_target_posterior(int, int)’:
bms.cpp:931:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
  931 |   for(int i=0; i < y->n_cols; i++) {
      |                ~~^~~~~~~~~~~
bms.cpp:940:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
  940 |     for(int j=0; j < M.n_cols; j++) {
      |                  ~~^~~~~~~~~~
bms.cpp:947:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
  947 |     for(int l=0; l < P[model].n_cols; l++) {
      |                  ~~^~~~~~~~~~~~~~~~~
bms.cpp: In member function ‘double BMS::log_target_pseudo(int, int)’:
bms.cpp:968:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
  968 |     for(int l=0; l < M.n_cols; l++) {
      |                  ~~^~~~~~~~~~
bms.cpp:974:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
  974 |     for(int l=0; l < P[model].n_cols; l++) {
      |                  ~~^~~~~~~~~~~~~~~~~
bms.cpp: In member function ‘void BMS::print_pseudo()’:
bms.cpp:1086:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
 1086 |     for(int l=0; l < M.n_cols; l++) {
      |                  ~~^~~~~~~~~~
bms.cpp:1089:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
 1089 |     for(int l=0; l < P[model].n_cols; l++) {
      |                  ~~^~~~~~~~~~~~~~~~~
bms.cpp:1100:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
 1100 |   for(int i=0; i < y->n_rows; i++) {
      |                ~~^~~~~~~~~~~
bms.cpp:1103:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
 1103 |       for(int l=0; l < M.n_cols; l++) {
      |                    ~~^~~~~~~~~~
bms.cpp:1106:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
 1106 |       for(int l=0; l < P[model].n_cols; l++) {
      |                    ~~^~~~~~~~~~~~~~~~~
bms.cpp: In constructor ‘BMS::BMS(const arma::Mat<double>*, const arma::Mat<double>&, arma::Mat<double>, arma::Mat<double>, arma::Mat<double>, arma::Mat<int>, double, double, double, std::string, gsl_rng**, int, bool)’:
bms.cpp:1188:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
 1188 |     for(int i=0; i < y->n_cols; i++) {
      |                  ~~^~~~~~~~~~~
bms.cpp:1192:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int, std::allocator<int> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
 1192 |         if(C(i,model)+1 > _n.size()) {
      |            ~~~~~~~~~~~~~^~~~~~~~~~~
bms.cpp: In member function ‘void BMS::initialise_streams(std::string)’:
bms.cpp:1348:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
 1348 |   for(int i=0; i < M.n_cols; i++) {
      |                ~~^~~~~~~~~~
bms.cpp:1354:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
 1354 |   for(int i=0; i < M.n_cols; i++) {
      |                ~~^~~~~~~~~~
bms.cpp:1360:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
 1360 |   for(int i=0; i < P[0].n_cols; i++) {
      |                ~~^~~~~~~~~~~~~
bms.cpp:1366:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
 1366 |   for(int i=0; i < P[1].n_cols; i++) {
      |                ~~^~~~~~~~~~~~~
bms.cpp:1372:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
 1372 |   for(int i=0; i < P[0].n_cols; i++) {
      |                ~~^~~~~~~~~~~~~
bms.cpp:1378:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
 1378 |   for(int i=0; i < P[1].n_cols; i++) {
      |                ~~^~~~~~~~~~~~~
g++ -DVERSION=1.0.11 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fopenmp -O3 fasta.o hitsio.o bam2hits.cpp -o ../bin/bam2hits -lgsl -lgslcblas -lboost_regex -lhts -lboost_iostreams -lflexiblas -lflexiblas -Wl,--as-needed -lz -lgfortran
bam2hits.cpp: In function ‘void outputMergeHeaders(std::vector<FastaRecord>&, char, const char*, bool, HitsfileWriter&)’:
bam2hits.cpp:109:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<FastaRecord>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  109 |   for(int i=0; i < sortedfastas.size()-1; i++) {
      |                ~~^~~~~~~~~~~~~~~~~~~~~~~
bam2hits.cpp:119:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<FastaRecord>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  119 |       for(int j=0; j < curSet.size()-1; j++) {
      |                    ~~^~~~~~~~~~~~~~~~~
bam2hits.cpp:137:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<FastaRecord>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  137 |   for(int j=0; j < curSet.size()-1; j++) {
      |                ~~^~~~~~~~~~~~~~~~~
bam2hits.cpp: In function ‘std::vector<Alignment> repetitiveTranscriptFilter(std::vector<Alignment>&, int)’:
bam2hits.cpp:218:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<Alignment>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  218 |   for(int j=0; j < alns.size(); j++) {
      |                ~~^~~~~~~~~~~~~
bam2hits.cpp:219:10: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  219 |     if(i < torem.size() && j==torem[i]) {
      |        ~~^~~~~~~~~~~~~~
bam2hits.cpp: In function ‘int main(int, char**)’:
bam2hits.cpp:518:15: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::__cxx11::basic_string<char>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  518 |         if(_B != tg[0].size()-2) {
      |            ~~~^~~~~~~~~~~~~~~~~
bam2hits.cpp:520:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::__cxx11::basic_string<char>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  520 |           if(_A == tg[0].size()-2) {
      |              ~~~^~~~~~~~~~~~~~~~~
bam2hits.cpp:522:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::__cxx11::basic_string<char>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  522 |             if(_A != tg[1].size()-2) {
      |                ~~~^~~~~~~~~~~~~~~~~
bam2hits.cpp:558:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  558 |       for(int i=1; i < tokens2.size(); i++) {
      |                    ~~^~~~~~~~~~~~~~~~
bam2hits.cpp:609:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<FastaRecord>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  609 |     for(int i=0; i < fastas.size(); i++) {
      |                  ~~^~~~~~~~~~~~~~~
bam2hits.cpp:645:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<FastaRecord>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  645 |     for(int i=0;i < fastas.size(); i++) transcriptCounts[i] /= (double)fastas[i].seq().size();
      |                 ~~^~~~~~~~~~~~~~~
bam2hits.cpp:659:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<FastaRecord>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  659 |     for(int i=0; i < fastas.size(); i++) {
      |                  ~~^~~~~~~~~~~~~~~
bam2hits.cpp:662:25: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::__cxx11::basic_string<char>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  662 |         for(int j =0; j < fastas[i].seq().size(); j++) {
      |                       ~~^~~~~~~~~~~~~~~~~~~~~~~~
bam2hits.cpp:663:44: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::__cxx11::basic_string<char>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  663 |           int tag = (j <= MSEQ_BEFORE || j >= fastas[i].seq().size()-MSEQ_AFTER) ? -2 : 0;
      |                                          ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
bam2hits.cpp:791:36: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::__cxx11::basic_string<char>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  791 |       for(int j=MSEQ_BEFORE + 1; j <= fastas[i].seq().length()-MSEQ_AFTER; j++) {
      |                                  ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
bam2hits.cpp:920:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  920 |     for(int j=1; j < frequencies.size()-WINDOWFORISIZEMODE + 1; j++) {
      |                  ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
bam2hits.cpp:948:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  948 |     for(int i=0; i < testIsizes.size(); i++) {
      |                  ~~^~~~~~~~~~~~~~~~~~~
bam2hits.cpp:959:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  959 |     for(int i=0; i < heights.size(); i++) {
      |                  ~~^~~~~~~~~~~~~~~~
bam2hits.cpp:997:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::__cxx11::basic_string<char>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  997 |       for(int fl=1; fl <= (it->seq()).size(); fl++) {
      |                     ~~~^~~~~~~~~~~~~~~~~~~~~
bam2hits.cpp:1091:56: warning: comparing the result of pointer addition ‘(bam_aux_get(((const bam1_t*)line), ((const char*)"NM")) + ((sizetype)ait.__gnu_cxx::__normal_iterator<Alignment*, std::vector<Alignment> >::operator->()->Alignment::NM()))’ and NULL [-Waddress]
 1091 |             ait->NM(ait->NM() + bam_aux_get(line,"NM") == NULL ? 0 : bam_aux2i(bam_aux_get(line,"NM")));
      |                                                        ^
g++ -DVERSION=1.0.11 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -O3 fasta.o extract_transcripts.cpp -o ../bin/extract_transcripts
extract_transcripts.cpp: In function ‘int main(int, char**)’:
extract_transcripts.cpp:122:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  122 |       for(int i=0; i < tokens2.size(); i++) {
      |                    ~~^~~~~~~~~~~~~~~~
extract_transcripts.cpp:169:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  169 |     for(int i=0; i < tokens.size(); i++) {
      |                  ~~^~~~~~~~~~~~~~~
extract_transcripts.cpp:195:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  195 |       for(int i=0; i < it->starts()->size(); i++) {
      |                    ~~^~~~~~~~~~~~~~~~~~~~~~
extract_transcripts.cpp:203:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::__cxx11::basic_string<char>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  203 |       while(faline < stitch.size()) {
      |             ~~~~~~~^~~~~~~~~~~~~~~
extract_transcripts.cpp:108:7: warning: unused variable ‘line’ [-Wunused-variable]
  108 |   int line=0;
      |       ^~~~
g++ -DVERSION=1.0.11 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fopenmp -O3 hitsio.o hitstools.cpp -o ../bin/hitstools -lgsl -lgslcblas -lboost_regex -lhts -lboost_iostreams -lflexiblas -lflexiblas -Wl,--as-needed -lz -lgfortran
hitstools.cpp: In function ‘void convert(char*, std::string)’:
hitstools.cpp:51:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   51 |         for(int i = 0; i < transcriptName.size(); i++) {
      |                        ~~^~~~~~~~~~~~~~~~~~~~~~~
hitstools.cpp: In function ‘int main(int, char**)’:
hitstools.cpp:96:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
   96 |                 for(int i = 0; i < transcriptName.size(); i++) {
      |                                ~~^~~~~~~~~~~~~~~~~~~~~~~
hitstools.cpp:136:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  136 |     for(int i = 0; i < transcriptName.size(); i++) {
      |                    ~~^~~~~~~~~~~~~~~~~~~~~~~
g++ -DVERSION=1.0.11 -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -fopenmp -O2 bms.o mmdiff.cpp -o ../bin/mmdiff -lgsl -lgslcblas -lboost_regex -lhts -lboost_iostreams -lflexiblas -lflexiblas -Wl,--as-needed -lz -lgfortran
mmdiff.cpp: In function ‘void parse_mmseq(std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >, std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >&, arma::Mat<double>&, arma::Mat<double>&, arma::Mat<double>&, int, int, double, bool)’:
mmdiff.cpp:100:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  100 |   for(int i=0; i < filenames.size(); i++) {
      |                ~~^~~~~~~~~~~~~~~~~~
mmdiff.cpp:111:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  111 |     for(int j=0; j < tokens.size(); j++) {
      |                  ~~^~~~~~~~~~~~~~~
mmdiff.cpp:138:16: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  138 |       if(k + 1 > features.size()) {
      |          ~~~~~~^~~~~~~~~~~~~~~~~
mmdiff.cpp:147:14: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
  147 |       if(k+1 > y.n_rows) {
      |          ~~~~^~~~~~~~~~
mmdiff.cpp:152:20: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses]
  152 |       if(!useprops && tokens[lmg_ind]=="NA" || useprops && tokens[mp_ind]=="NA") {
      |          ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
mmdiff.cpp:173:62: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
  173 |   if(range_start >=0 && range_end > range_start && range_end < y.n_rows) {
      |                                                    ~~~~~~~~~~^~~~~~~~~~
mmdiff.cpp:94:46: warning: variable ‘mcse_ind’ set but not used [-Wunused-but-set-variable]
   94 |   int feature_ind=-1, lmg_ind=-1, sd_ind=-1, mcse_ind=-1, iact_ind=-1, mp_ind=-1, sp_ind=-1, uh_ind=-1;
      |                                              ^~~~~~~~
mmdiff.cpp:94:59: warning: variable ‘iact_ind’ set but not used [-Wunused-but-set-variable]
   94 |   int feature_ind=-1, lmg_ind=-1, sd_ind=-1, mcse_ind=-1, iact_ind=-1, mp_ind=-1, sp_ind=-1, uh_ind=-1;
      |                                                           ^~~~~~~~
mmdiff.cpp: In function ‘void apply_normalisation(std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >, arma::Mat<double>&, arma::Mat<double>&, double)’:
mmdiff.cpp:212:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
  212 |   for(int i=0; i < uh.n_rows; i++) {
      |                ~~^~~~~~~~~~~
mmdiff.cpp:214:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
  214 |     for(int j=0; j < uh.n_cols; j++) {
      |                  ~~^~~~~~~~~~~
mmdiff.cpp:230:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int, std::allocator<int> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  230 |   for(int i=0; i < use.size(); i++) {
      |                ~~^~~~~~~~~~~~
mmdiff.cpp:232:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
  232 |     for(int j=0; j < y.n_cols; j++) {
      |                  ~~^~~~~~~~~~
mmdiff.cpp:239:28: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
  239 |   for(int sample=0; sample < y.n_cols; sample++) {
      |                     ~~~~~~~^~~~~~~~~~
mmdiff.cpp:241:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int, std::allocator<int> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  241 |     for(int i=0; i < use.size(); i++) {
      |                  ~~^~~~~~~~~~~~
mmdiff.cpp:246:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
  246 |     for(int i=0; i < y.n_rows; i++) {
      |                  ~~^~~~~~~~~~
mmdiff.cpp: In function ‘void apply_permutation(arma::Mat<double>&, arma::Mat<double>&)’:
mmdiff.cpp:257:17: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
  257 |   for(int j=0; j< y.n_cols; j++) randinds.push_back(j);
      |                ~^~~~~~~~~~
mmdiff.cpp:258:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
  258 |   for(int i=0; i < y.n_rows; i++) {
      |                ~~^~~~~~~~~~
mmdiff.cpp:259:19: warning: ‘void std::random_shuffle(_RAIter, _RAIter) [with _RAIter = __gnu_cxx::__normal_iterator<int*, vector<int, allocator<int> > >]’ is deprecated: use 'std::shuffle' instead [-Wdeprecated-declarations]
  259 |     random_shuffle(randinds.begin(), randinds.end());
      |     ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/14/algorithm:61,
                 from mmdiff.cpp:31:
/usr/include/c++/14/bits/stl_algo.h:4491:5: note: declared here
 4491 |     random_shuffle(_RandomAccessIterator __first, _RandomAccessIterator __last)
      |     ^~~~~~~~~~~~~~
mmdiff.cpp:260:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
  260 |     for(int j=0; j < y.n_cols; j++) {
      |                  ~~^~~~~~~~~~
mmdiff.cpp: In function ‘void parse_matrices(std::string, arma::Mat<double>&, arma::Mat<double>&, arma::Mat<double>&, arma::Mat<int>&, int)’:
mmdiff.cpp:310:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  310 |     for(int t=0; t < tokens.size(); t++) {
      |                  ~~^~~~~~~~~~~~~~~
mmdiff.cpp: In function ‘int main(int, char**)’:
mmdiff.cpp:420:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  420 |       for(int i=0; i < arguments.size(); i++) {
      |                    ~~^~~~~~~~~~~~~~~~~~
mmdiff.cpp:431:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  431 |       for(int i=0; i < arguments.size(); i++) {
      |                    ~~^~~~~~~~~~~~~~~~~~
mmdiff.cpp:439:16: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  439 |       while(ss < arguments.size()) {
      |             ~~~^~~~~~~~~~~~~~~~~~
mmdiff.cpp:451:13: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  451 |       if(ss != arguments.size()) {
      |          ~~~^~~~~~~~~~~~~~~~~~~
mmdiff.cpp:578:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  578 |   for(int i=0; i < arguments.size(); i++) {
      |                ~~^~~~~~~~~~~~~~~~~~
mmdiff.cpp:640:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int, std::allocator<int> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  640 |     for(int i=0; i < simple_de.size(); i++) {
      |                  ~~^~~~~~~~~~~~~~~~~~
mmdiff.cpp:759:17: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses]
  759 |     if(inburnin && iter == OUTLEN/10 || !inburnin && iter==tuneiters) {
      |        ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~
mmdiff.cpp:764:32: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  764 |     for(int feature=0; feature < features.size(); feature++) {
      |                        ~~~~~~~~^~~~~~~~~~~~~~~~~
mmdiff.cpp:837:17: warning: suggest parentheses around ‘&&’ within ‘||’ [-Wparentheses]
  837 |     if(inburnin && iter % subsample_burnin ==0 || !inburnin && iter >= tuneiters && (iter - tuneiters) % subsample_iter == 0) {
      |        ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
mmdiff.cpp:886:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
  886 |       for(int l=0; l < M.n_cols; l++) {
      |                    ~~^~~~~~~~~~
mmdiff.cpp:898:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  898 |   for(int f=0; f < samplenames.size(); f++) {
      |                ~~^~~~~~~~~~~~~~~~~~~~
mmdiff.cpp:902:22: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const std::__cxx11::basic_string<char>::size_type’ {aka ‘const long unsigned int’} [-Wsign-compare]
  902 |       found2 = found2==string::npos ? -1 : found2;
      |                ~~~~~~^~~~~~~~~~~~~~
mmdiff.cpp:907:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  907 |   for(int f=0; f < samplenames.size(); f++) {
      |                ~~^~~~~~~~~~~~~~~~~~~~
mmdiff.cpp:909:10: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  909 |     if(f < samplenames.size()-1) cout << "\t";
      |        ~~^~~~~~~~~~~~~~~~~~~~~~
mmdiff.cpp:914:30: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  914 |   for(int feature=0; feature < features.size(); feature++) {
      |                      ~~~~~~~~^~~~~~~~~~~~~~~~~
mmdiff.cpp:926:24: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const arma::uword’ {aka ‘const long long unsigned int’} [-Wsign-compare]
  926 |         for(int l=0; l < M.n_cols; l++) {
      |                      ~~^~~~~~~~~~
mmdiff.cpp:936:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  936 |     for(int f=0; f < samplenames.size(); f++) {
      |                  ~~^~~~~~~~~~~~~~~~~~~~
mmdiff.cpp:939:20: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  939 |     for(int f=0; f < samplenames.size(); f++) {
      |                  ~~^~~~~~~~~~~~~~~~~~~~
mmdiff.cpp:941:12: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  941 |       if(f < samplenames.size()-1) cout << "\t";
      |          ~~^~~~~~~~~~~~~~~~~~~~~~
mmdiff.cpp:951:34: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<std::__cxx11::basic_string<char>, std::allocator<std::__cxx11::basic_string<char> > >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  951 |       for(int feature=0; feature < features.size(); feature++) {
      |                          ~~~~~~~~^~~~~~~~~~~~~~~~~
/usr/bin/ld: /tmp/ccmbqMwO.ltrans0.ltrans.o: in function `main':
/builddir/build/BUILD/mmseq-1.0.11-build/mmseq-1.0.11/src/bam2hits.cpp:653:(.text.startup+0x25dd): warning: the use of `tmpnam' is dangerous, better use `mkstemp'
+ RPM_EC=0
++ jobs -p
+ exit 0
Executing(%install): /bin/sh -e /var/tmp/rpm-tmp.j5Z9aB
+ umask 022
+ cd /builddir/build/BUILD/mmseq-1.0.11-build
+ '[' /builddir/build/BUILD/mmseq-1.0.11-build/BUILDROOT '!=' / ']'
+ rm -rf /builddir/build/BUILD/mmseq-1.0.11-build/BUILDROOT
++ dirname /builddir/build/BUILD/mmseq-1.0.11-build/BUILDROOT
+ mkdir -p /builddir/build/BUILD/mmseq-1.0.11-build
+ mkdir /builddir/build/BUILD/mmseq-1.0.11-build/BUILDROOT
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ export CFLAGS
+ CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ export CXXFLAGS
+ FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules '
+ export FFLAGS
+ FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules '
+ export FCFLAGS
+ VALAFLAGS=-g
+ export VALAFLAGS
+ RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none -Cforce-frame-pointers=yes -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn'
+ export RUSTFLAGS
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed  -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ export LDFLAGS
+ LT_SYS_LIBRARY_PATH=/usr/lib64:
+ export LT_SYS_LIBRARY_PATH
+ CC=gcc
+ export CC
+ CXX=g++
+ export CXX
+ cd mmseq-1.0.11
+ rm -rf /builddir/build/BUILD/mmseq-1.0.11-build/BUILDROOT
+ mkdir -p /builddir/build/BUILD/mmseq-1.0.11-build/BUILDROOT/usr/bin
+ install -p -m 0755 bin/bam2hits /builddir/build/BUILD/mmseq-1.0.11-build/BUILDROOT/usr/bin
+ install -p -m 0755 bin/extract_transcripts /builddir/build/BUILD/mmseq-1.0.11-build/BUILDROOT/usr/bin
+ install -p -m 0755 bin/hitstools /builddir/build/BUILD/mmseq-1.0.11-build/BUILDROOT/usr/bin
+ install -p -m 0755 bin/mmcollapse /builddir/build/BUILD/mmseq-1.0.11-build/BUILDROOT/usr/bin
+ install -p -m 0755 bin/mmdiff /builddir/build/BUILD/mmseq-1.0.11-build/BUILDROOT/usr/bin
+ install -p -m 0755 bin/mmseq /builddir/build/BUILD/mmseq-1.0.11-build/BUILDROOT/usr/bin
+ install -p -m 0755 bin/offsetGTF /builddir/build/BUILD/mmseq-1.0.11-build/BUILDROOT/usr/bin
+ install -p -m 0755 bin/t2g_hits /builddir/build/BUILD/mmseq-1.0.11-build/BUILDROOT/usr/bin
+ install -p -m 0755 bin/fastagrep.sh bin/mouse_strain_transcriptome.sh bin/usage.sh /builddir/build/BUILD/mmseq-1.0.11-build/BUILDROOT/usr/bin
+ install -p -m 0755 bin/filterGTF.rb bin/haploref.rb bin/testregexp.rb /builddir/build/BUILD/mmseq-1.0.11-build/BUILDROOT/usr/bin
+ install -p -m 0755 bin/ensembl_gtf_to_gff.pl /builddir/build/BUILD/mmseq-1.0.11-build/BUILDROOT/usr/bin
+ /usr/bin/find-debuginfo -j2 --strict-build-id -m -i --build-id-seed 1.0.11-19.fc41 --unique-debug-suffix -1.0.11-19.fc41.x86_64 --unique-debug-src-base mmseq-1.0.11-19.fc41.x86_64 --run-dwz --dwz-low-mem-die-limit 10000000 --dwz-max-die-limit 110000000 -S debugsourcefiles.list /builddir/build/BUILD/mmseq-1.0.11-build/mmseq-1.0.11
find-debuginfo: starting
Extracting debug info from 8 files
DWARF-compressing 8 files
sepdebugcrcfix: Updated 8 CRC32s, 0 CRC32s did match.
Creating .debug symlinks for symlinks to ELF files
Copying sources found by 'debugedit -l' to /usr/src/debug/mmseq-1.0.11-19.fc41.x86_64
542 blocks
find-debuginfo: done
+ /usr/lib/rpm/check-buildroot
+ /usr/lib/rpm/redhat/brp-ldconfig
+ /usr/lib/rpm/brp-compress
+ /usr/lib/rpm/redhat/brp-strip-lto /usr/bin/strip
+ /usr/lib/rpm/brp-strip-static-archive /usr/bin/strip
+ /usr/lib/rpm/check-rpaths
+ /usr/lib/rpm/redhat/brp-mangle-shebangs
mangling shebang in /usr/bin/fastagrep.sh from /bin/bash to #!/usr/bin/bash
mangling shebang in /usr/bin/mouse_strain_transcriptome.sh from /bin/sh to #!/usr/bin/sh
mangling shebang in /usr/bin/usage.sh from /bin/bash to #!/usr/bin/bash
mangling shebang in /usr/bin/filterGTF.rb from /usr/bin/env ruby to #!/usr/bin/ruby
mangling shebang in /usr/bin/haploref.rb from /usr/bin/env ruby to #!/usr/bin/ruby
mangling shebang in /usr/bin/testregexp.rb from /usr/bin/env ruby to #!/usr/bin/ruby
mangling shebang in /usr/bin/ensembl_gtf_to_gff.pl from /usr/bin/env perl to #!/usr/bin/perl
+ /usr/lib/rpm/brp-remove-la-files
+ env /usr/lib/rpm/redhat/brp-python-bytecompile '' 1 0 -j2
+ /usr/lib/rpm/redhat/brp-python-hardlink
+ /usr/bin/add-determinism --brp -j2 /builddir/build/BUILD/mmseq-1.0.11-build/BUILDROOT
Cannot initialize handler pyc: ModuleNotFoundError: No module named 'marshalparser'
[src/multiprocess.rs:66:9] &cmd = Command {
    program: "/usr/bin/add-determinism",
    args: [
        "/usr/bin/add-determinism",
        "--socket",
        "3",
        "--brp",
        "--handler",
        "ar,jar,javadoc",
    ],
    env: CommandEnv {
        clear: false,
        vars: {
            "SOURCE_DATE_EPOCH": Some(
                "1706140800",
            ),
        },
    },
    create_pidfd: false,
}
Bye!
Bye!
Reading /builddir/build/BUILD/mmseq-1.0.11-build/SPECPARTS/rpm-debuginfo.specpart
Executing(%check): /bin/sh -e /var/tmp/rpm-tmp.H5KP1C
+ umask 022
+ cd /builddir/build/BUILD/mmseq-1.0.11-build
+ CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ export CFLAGS
+ CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer '
+ export CXXFLAGS
+ FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules '
+ export FFLAGS
+ FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -m64 -march=x86-64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -mtls-dialect=gnu2 -fno-omit-frame-pointer -mno-omit-leaf-frame-pointer -I/usr/lib64/gfortran/modules '
+ export FCFLAGS
+ VALAFLAGS=-g
+ export VALAFLAGS
+ RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none -Cforce-frame-pointers=yes -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn'
+ export RUSTFLAGS
+ LDFLAGS='-Wl,-z,relro -Wl,--as-needed  -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1  -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes '
+ export LDFLAGS
+ LT_SYS_LIBRARY_PATH=/usr/lib64:
+ export LT_SYS_LIBRARY_PATH
+ CC=gcc
+ export CC
+ CXX=g++
+ export CXX
+ cd mmseq-1.0.11
++ bin/mmseq --version
++ true
+ test mmseq-1.0.11 = mmseq-1.0.11
+ RPM_EC=0
++ jobs -p
+ exit 0
Processing files: mmseq-1.0.11-19.fc41.x86_64
Executing(%doc): /bin/sh -e /var/tmp/rpm-tmp.qMBV04
+ umask 022
+ cd /builddir/build/BUILD/mmseq-1.0.11-build
+ cd mmseq-1.0.11
+ DOCDIR=/builddir/build/BUILD/mmseq-1.0.11-build/BUILDROOT/usr/share/doc/mmseq
+ export LC_ALL=C.UTF-8
+ LC_ALL=C.UTF-8
+ export DOCDIR
+ /usr/bin/mkdir -p /builddir/build/BUILD/mmseq-1.0.11-build/BUILDROOT/usr/share/doc/mmseq
+ cp -pr /builddir/build/BUILD/mmseq-1.0.11-build/mmseq-1.0.11/README.md /builddir/build/BUILD/mmseq-1.0.11-build/BUILDROOT/usr/share/doc/mmseq
+ cp -pr /builddir/build/BUILD/mmseq-1.0.11-build/mmseq-1.0.11/COPYING /builddir/build/BUILD/mmseq-1.0.11-build/BUILDROOT/usr/share/doc/mmseq
+ cp -pr /builddir/build/BUILD/mmseq-1.0.11-build/mmseq-1.0.11/doc /builddir/build/BUILD/mmseq-1.0.11-build/BUILDROOT/usr/share/doc/mmseq
+ RPM_EC=0
++ jobs -p
+ exit 0
Provides: mmseq = 1.0.11-19.fc41 mmseq(x86-64) = 1.0.11-19.fc41
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Requires: /usr/bin/bash /usr/bin/perl /usr/bin/ruby /usr/bin/sh libboost_iostreams.so.1.83.0()(64bit) libboost_regex.so.1.83.0()(64bit) libc.so.6()(64bit) libc.so.6(GLIBC_2.14)(64bit) libc.so.6(GLIBC_2.2.5)(64bit) libc.so.6(GLIBC_2.3)(64bit) libc.so.6(GLIBC_2.3.4)(64bit) libc.so.6(GLIBC_2.32)(64bit) libc.so.6(GLIBC_2.33)(64bit) libc.so.6(GLIBC_2.34)(64bit) libc.so.6(GLIBC_2.38)(64bit) libc.so.6(GLIBC_2.4)(64bit) libflexiblas.so.3()(64bit) libgcc_s.so.1()(64bit) libgcc_s.so.1(GCC_3.0)(64bit) libgcc_s.so.1(GCC_3.3.1)(64bit) libgomp.so.1()(64bit) libgomp.so.1(GOMP_1.0)(64bit) libgomp.so.1(GOMP_4.0)(64bit) libgomp.so.1(OMP_1.0)(64bit) libgsl.so.27()(64bit) libgslcblas.so.0()(64bit) libhts.so.3()(64bit) libm.so.6()(64bit) libm.so.6(GLIBC_2.2.5)(64bit) libm.so.6(GLIBC_2.29)(64bit) libstdc++.so.6()(64bit) libstdc++.so.6(CXXABI_1.3)(64bit) libstdc++.so.6(CXXABI_1.3.15)(64bit) libstdc++.so.6(CXXABI_1.3.8)(64bit) libstdc++.so.6(CXXABI_1.3.9)(64bit) libstdc++.so.6(GLIBCXX_3.4)(64bit) libstdc++.so.6(GLIBCXX_3.4.11)(64bit) libstdc++.so.6(GLIBCXX_3.4.15)(64bit) libstdc++.so.6(GLIBCXX_3.4.20)(64bit) libstdc++.so.6(GLIBCXX_3.4.21)(64bit) libstdc++.so.6(GLIBCXX_3.4.26)(64bit) libstdc++.so.6(GLIBCXX_3.4.29)(64bit) libstdc++.so.6(GLIBCXX_3.4.30)(64bit) libstdc++.so.6(GLIBCXX_3.4.32)(64bit) libstdc++.so.6(GLIBCXX_3.4.9)(64bit) perl(strict) rtld(GNU_HASH)
Processing files: mmseq-debugsource-1.0.11-19.fc41.x86_64
Provides: mmseq-debugsource = 1.0.11-19.fc41 mmseq-debugsource(x86-64) = 1.0.11-19.fc41
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Processing files: mmseq-debuginfo-1.0.11-19.fc41.x86_64
Provides: debuginfo(build-id) = 608e821f89293d587be852881eacded426e825a9 debuginfo(build-id) = 69a26f047e4932ef7b5540484075b5643f6fe28b debuginfo(build-id) = 7d0ad6b02360a5e3f649a408e1fae1c6e7e1a5c3 debuginfo(build-id) = 867fa41d1c4a81d8e651fa36d4919c06e485abb1 debuginfo(build-id) = bd252e3cf9e07c1861dadecab5c87e272bc68754 debuginfo(build-id) = bef4381a5cada94ba45178dbb6670011aa60a6e8 debuginfo(build-id) = e28d87d7427324b64622eb59c3085d0374682403 debuginfo(build-id) = e91d422f267a543c5caad40c19012fdd51ea2a3f mmseq-debuginfo = 1.0.11-19.fc41 mmseq-debuginfo(x86-64) = 1.0.11-19.fc41
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Recommends: mmseq-debugsource(x86-64) = 1.0.11-19.fc41
Checking for unpackaged file(s): /usr/lib/rpm/check-files /builddir/build/BUILD/mmseq-1.0.11-build/BUILDROOT
Wrote: /builddir/build/RPMS/mmseq-1.0.11-19.fc41.x86_64.rpm
Wrote: /builddir/build/RPMS/mmseq-debugsource-1.0.11-19.fc41.x86_64.rpm
Wrote: /builddir/build/RPMS/mmseq-debuginfo-1.0.11-19.fc41.x86_64.rpm
Executing(rmbuild): /bin/sh -e /var/tmp/rpm-tmp.NSzyGF
+ umask 022
+ cd /builddir/build/BUILD/mmseq-1.0.11-build
+ test -d /builddir/build/BUILD/mmseq-1.0.11-build
+ /usr/bin/chmod -Rf a+rX,u+w,g-w,o-w /builddir/build/BUILD/mmseq-1.0.11-build
+ rm -rf /builddir/build/BUILD/mmseq-1.0.11-build
+ RPM_EC=0
++ jobs -p
+ exit 0
Finish: rpmbuild mmseq-1.0.11-19.fc41.src.rpm
Finish: build phase for mmseq-1.0.11-19.fc41.src.rpm
INFO: chroot_scan: 3 files copied to /var/lib/copr-rpmbuild/results/chroot_scan
INFO: /var/lib/mock/fedora-39-x86_64-1717081834.800473/root/var/log/dnf.log
/var/lib/mock/fedora-39-x86_64-1717081834.800473/root/var/log/dnf.librepo.log
/var/lib/mock/fedora-39-x86_64-1717081834.800473/root/var/log/dnf.rpm.log
INFO: Done(/var/lib/copr-rpmbuild/results/mmseq-1.0.11-19.fc41.src.rpm) Config(child) 1 minutes 37 seconds
INFO: Results and/or logs in: /var/lib/copr-rpmbuild/results
INFO: Cleaning up build root ('cleanup_on_success=True')
Start: clean chroot
INFO: unmounting tmpfs.
Finish: clean chroot
Finish: run
Running RPMResults tool
Package info:
{
    "packages": [
        {
            "name": "mmseq",
            "epoch": null,
            "version": "1.0.11",
            "release": "19.fc41",
            "arch": "src"
        },
        {
            "name": "mmseq",
            "epoch": null,
            "version": "1.0.11",
            "release": "19.fc41",
            "arch": "x86_64"
        },
        {
            "name": "mmseq-debugsource",
            "epoch": null,
            "version": "1.0.11",
            "release": "19.fc41",
            "arch": "x86_64"
        },
        {
            "name": "mmseq-debuginfo",
            "epoch": null,
            "version": "1.0.11",
            "release": "19.fc41",
            "arch": "x86_64"
        }
    ]
}
RPMResults finished